Last active
July 12, 2023 08:55
-
-
Save lindenb/83196adbb034ef5874086d10dd9772ac to your computer and use it in GitHub Desktop.
Forum: Programming language use distribution from recent programs / articles https://www.biostars.org/p/251002/#251056 pubmed language code
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| -e PMID | LANG | TITLE | YEAR | CONTEXT | |
|---|---|---|---|---|---|
| 29490021 | r | ShinyKGode: an Interactive Application for ODE Parameter Inference Using Gradient Matching. | 2018 | the [R package] for shiny | |
| 29490015 | r | Isoform-level gene expression patterns in single-cell RNA-sequencing data. | 2018 | nted as a [R package] and is av | |
| 29490010 | python | SECLAF: A Webserver and Deep Neural Network Design Tool for Hierarchical Biological Sequence Classification. | 2018 | mented in [python], and is a | |
| 29486711 | r | lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals. | 2018 | mms). the [R package] lme4 is a | |
| 29474733 | c | Bacmeta: simulator for genomic evolution in bacterial metapopulations. | 2018 | simulated [using C] ++ object | |
| 29474526 | r | IWTomics: testing high-resolution sequence-based Omics data at multiple locations and scales. | 2018 | le at the [Bioconductor] website ( | |
| 29462241 | r | flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry. | 2018 | ble as an [R package] on https: | |
| 29458351 | r | CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. | 2018 | cemitool [R package] provides | |
| 29447401 | r | RaMWAS: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms. | 2018 | conductor [R package] called ra | |
| 29444641 | java | Oasis 2: improved online analysis of small RNA-seq data. | 2018 | mented in [java], j2ee, my | |
| 29444641 | python | Oasis 2: improved online analysis of small RNA-seq data. | 2018 | e, mysql, [python], r, php a | |
| 29444641 | javascript | Oasis 2: improved online analysis of small RNA-seq data. | 2018 | , php and [javascript]. it is fr | |
| 29444236 | r | findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. | 2018 | [R package] of findgs | |
| 29444234 | python | ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. | 2018 | [python] software | |
| 29444205 | python | ssbio: A Python Framework for Structural Systems Biology. | 2018 | ssbio: a [python] framework | |
| 29438558 | r | KMgene: a unified R package for gene-based association analysis for complex traits. | 2018 | a unified [R package] for gene- | |
| 29438498 | r | chromswitch: A flexible method to detect chromatin state switches. | 2018 | ted as an [R package] available | |
| 29432517 | mathlab | Spectral clustering based on learning similarity matrix. | 2018 | mented in [matlab]. the sour | |
| 29432514 | r | Improving SNP Prioritization and Pleiotropic Architecture Estimation by Incorporating Prior Knowledge Using graph-GPA. | 2018 | ted as an [R package] 'ggpa', w | |
| 29420693 | r | FWER and FDR Control When Testing Multiple Mediators. | 2018 | [R package] multimed | |
| 29420676 | mathlab | Principal Metabolic Flux Mode Analysis. | 2018 | [matlab] software | |
| 29415263 | mathlab | scEpath: Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. | 2018 | a [matlab] package o | |
| 29401218 | javascript | MutHTP: Mutations in Human Transmembrane Proteins. | 2018 | , php and [javascript] and suppo | |
| 29401212 | python | GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. | 2018 | ritten in [python], javascri | |
| 29401212 | javascript | GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. | 2018 | n python, [javascript] library d | |
| 29394323 | python | pymzML v2.0: introducing a highly compressed and seekable gzip format. | 2018 | requires [python3].4+ and op | |
| 29390967 | javascript | Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. | 2018 | e adopted [javascript] object no | |
| 29385404 | python | TOXsIgN: a cross-species repository for toxicogenomic signatures. | 2018 | mented in [python], javascri | |
| 29385404 | javascript | TOXsIgN: a cross-species repository for toxicogenomic signatures. | 2018 | n python, [javascript], and mong | |
| 29385403 | r | TSAPA: identification of tissue-specific alternative polyadenylation sites in plants. | 2018 | eloped an [R package] called ts | |
| 29361904 | python | Spherical: an iterative workflow for assembling metagenomic datasets. | 2018 | mented in [python], to addre | |
| 29360996 | r | Feature Specific Quantile Normalization Enables Cross-Platform Classification of Molecular Subtypes using Gene Expression Data. | 2018 | ted as an [R package] to cran. | |
| 29360936 | python | Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. | 2018 | platform, [python] package c | |
| 29357822 | javascript | MutScan: fast detection and visualization of target mutations by scanning FASTQ data. | 2018 | html and [javascript]. algorith | |
| 29346510 | java | VIPER: a web application for rapid expert review of variant calls. | 2018 | mented in [java] and javas | |
| 29346510 | javascript | VIPER: a web application for rapid expert review of variant calls. | 2018 | java and [javascript] and is fr | |
| 29346509 | r | A distance-based approach for testing the mediation effect of the human microbiome. | 2018 | an [R package] medtest | |
| 29342241 | java | iPat: Intelligent Prediction and Association Tool for Genomic Research. | 2018 | ritten in [java] for adapt | |
| 29342236 | r | MAGNAMWAR: An R package for genome-wide association studies of bacterial orthologs. | 2018 | amwar: an [R package] for genom | |
| 29342233 | r | QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. | 2018 | ntumclone [R package] are freel | |
| 29340616 | python | PyChimera: Use UCSF Chimera modules in any Python 2.7 project. | 2018 | es in any [python] 2.7 proje | |
| 29340599 | r | A benchmark study of scoring methods for non-coding mutations. | 2018 | ake, c ++ [and R] codes are | |
| 29334888 | r | diceR: an R package for class discovery using an ensemble driven approach. | 2018 | dicer: an [R package] for class | |
| 29329398 | python | LeNup: Learning Nucleosome positioning from DNA sequences with improved convolutional neural networks. | 2018 | ilable as [python] and lua s | |
| 29329372 | r | Enrichment analysis with EpiAnnotator. | 2018 | tor is an [R package] accompani | |
| 29315360 | r | CGManalyzer:an R package for analyzing continuous glucose monitoring studies. | 2018 | alyzer:an [R package] for analy | |
| 29310570 | r | Thresher: determining the number of clusters while removing outliers. | 2018 | ted in an [R package] called th | |
| 29309511 | r | DiffGraph: An R package for identifying gene network rewiring using differential graphical models. | 2017 | graph: an [R package] for ident | |
| 29300846 | python | ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. | 2017 | ritten in [python] and c ++ | |
| 29300845 | python | ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing. | 2017 | ) and the [python] package i | |
| 29297298 | mathlab | 2D-EM clustering approach for high-dimensional data through folding feature vectors. | 2017 | methods. [matlab] implement | |
| 29297297 | mathlab | Divisive hierarchical maximum likelihood clustering. | 2017 | logies. a [matlab] implement | |
| 29297289 | javascript | dBBQs: dataBase of Bacterial Quality scores. | 2017 | teractive [javascript] chart fra | |
| 29293946 | r | polyPK: An R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach. | 2017 | olypk: an [R package] for pharm | |
| 29293920 | java | Towards Self-Learning Based Hypotheses Generation in Biomedical Text Domain. | 2017 | relevant [java] codes are | |
| 29291710 | r | Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect. | 2018 | hod in an [R package] (triadsim | |
| 29280999 | r | Multiple hot-deck imputation for network inference from RNA sequencing data. | 2017 | ble as an [R package], rnaseqne | |
| 29280991 | r | R2DGC: Threshold-free peak alignment and identification for 2D gas chromatography mass spectrometry in R. | 2017 | eloped an [R package] that impl | |
| 29272352 | r | Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations. | 2017 | the [R package] is availa | |
| 29267850 | r | Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. | 2017 | pcake: an [R package] for query | |
| 29267848 | python | ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions. | 2017 | tandalone [python] package c | |
| 29258445 | java | A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. | 2017 | provide a [java] code of o | |
| 29253085 | python | JASPAR RESTful API: accessing JASPAR data from any programming language. | 2017 | mented in [python] using the | |
| 29253072 | r | K2 and K*2: Efficient alignment-free sequence similarity measurement based on Kendall statistics. | 2017 | ed in the [R language] as a pack | |
| 29244013 | java | Cache and energy efficient algorithms for Nussinov's RNA Folding. | 2017 | pose. the [java] versions | |
| 29244010 | mathlab | RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks. | 2017 | ampler in [matlab] and its e | |
| 29240889 | java | GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. | 2017 | mented in [java] 1.8, and | |
| 29237399 | r | Redundancy analysis allows improved detection of methylation changes in large genomic regions. | 2017 | n meal, a [Bioconductor] package d | |
| 29237398 | python | pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data. | 2017 | allelized [python] package t | |
| 29236977 | r | gene2drug: a Computational Tool for Pathway-based Rational Drug Repositioning. | 2017 | em.it. an [R package] is under | |
| 29236969 | r | DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification. | 2017 | rs at the [Bioconductor] open-sour | |
| 29236954 | python | NGLview - Interactive molecular graphics for Jupyter notebooks. | 2017 | /nglview. [python] packages | |
| 29236954 | javascript | NGLview - Interactive molecular graphics for Jupyter notebooks. | 2017 | -side and [javascript] on the cl | |
| 29228294 | bash | Accurate Mapping of tRNA Reads. | 2017 | both as a [bash] script an | |
| 29228182 | python | PEITH(Θ) - Perfecting Experiments with Information Theory in Python with GPU support. | 2017 | theory in [python] with gpu | |
| 29212440 | python | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. | 2017 | onomy), a [python] tool that | |
| 29206901 | mathlab | GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. | 2017 | range of [matlab] versions | |
| 29194472 | r | ThetaMater: Bayesian estimation of population size parameter θ from genomic data. | 2017 | en source [R package] comprisin | |
| 29194470 | r | iDINGO - Integrative Differential Network Analysis in Genomics with Shiny Application. | 2017 | he idingo [R package] to estima | |
| 29187149 | r | DBNorm: normalizing high-density oligonucleotide microarray data based on distributions. | 2017 | ted as an [R package], is an al | |
| 29187143 | python | DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. | 2017 | ritten in [python] and r, an | |
| 29187143 | r | DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. | 2017 | in python [and R], and is s | |
| 29186450 | java | SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. | 2017 | ritten in [java], that com | |
| 29186355 | mathlab | Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. | 2017 | s well as [matlab] implement | |
| 29186344 | perl | MOCASSIN-prot: A Multi-Objective Clustering Approach for Protein Similarity Networks. | 2017 | mented in [perl] and matla | |
| 29186344 | mathlab | MOCASSIN-prot: A Multi-Objective Clustering Approach for Protein Similarity Networks. | 2017 | perl and [matlab], is freel | |
| 29186339 | java | bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. | 2017 | or a pure [java] expressio | |
| 29186339 | javascript | bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. | 2017 | s using a [javascript] engine or | |
| 29186333 | python | FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web. | 2017 | kages and [python] libraries | |
| 29186328 | r | Meta-analytic Principal Component Analysis in Integrative Omics Application. | 2017 | an [R package] metapca i | |
| 29186322 | java | SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. | 2017 | ritten in [java] and freel | |
| 29186321 | java | Mapping-free variant calling using haplotype reconstruction from k-mer frequencies. | 2017 | ion for a [java] implement | |
| 29186298 | python | SimulaTE: Simulating complex landscapes of transposable elements of populations. | 2017 | mented in [python] and avail | |
| 29186290 | perl | scHiCNorm: A Software Package to Eliminate Systematic Biases in Single-Cell Hi-C Data. | 2017 | hicnorm/. [perl] scripts a | |
| 29186288 | java | Reproducible and flexible simulation experiments with ML-Rules and SESSL. | 2017 | mented in [java], sessl an | |
| 29186284 | c | CALQ: compression of quality values of aligned sequencing data. | 2017 | calq is [written in C] ++ and ca | |
| 29178844 | r | BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems. | 2017 | ilter: an [R package] for estim | |
| 29166858 | r | ADAGE signature analysis: differential expression analysis with data-defined gene sets. | 2017 | d both an [R package] (adagepat | |
| 29162056 | perl | Synima: a Synteny imaging tool for annotated genome assemblies. | 2017 | ritten in [perl], which us | |
| 29155928 | python | Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. | 2017 | e concise [python] package: | |
| 29151019 | r | bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests. | 2017 | rface: an [R package] for corre | |
| 29145823 | r | dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder. | 2017 | e applied [R language] software | |
| 29132318 | c++ | BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness. | 2017 | is a fast [C++] applicati | |
| 29126132 | python | Cost-effective and accurate method of measuring fetal fraction using SNP imputation. | 2017 | [python] source co | |
| 29121165 | python | PERF: An Exhaustive Algorithm for Ultra-Fast and Efficient Identification of Microsatellites from Large DNA Sequences. | 2017 | ed in the [python] programmi | |
| 29112706 | r | NanoStringNormCNV: Pre-processing of NanoString CNV data. | 2017 | rmcnv, an [R package] for pre-p | |
| 29110634 | java | JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals. | 2017 | a modular [java] backend w | |
| 29110634 | javascript | JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals. | 2017 | , modular [javascript] viewer fo | |
| 29106469 | python | DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. | 2017 | mented in [python] 3 and run | |
| 29106443 | r | Estimation of QTL heritability based on pooled sequencing data. | 2017 | uires the [R package] rootsolve | |
| 29106441 | python | orchid: a novel management, annotation, and machine learning framework for analyzing cancer mutations. | 2017 | orchid, a [python] based sof | |
| 29095980 | javascript | pedigreejs: a web-based graphical pedigree editor. | 2017 | ritten in [javascript], which us | |
| 29095974 | python | BEAM web server: A tool for structural RNA motif discovery. | 2017 | odejs and [python] with all | |
| 29092015 | java | MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. | 2018 | ritten in [java] and is pl | |
| 29092009 | r | Machine learning annotation of human branchpoints. | 2017 | ogramming [language r] and is fr | |
| 29091997 | r | Efficient comparative phylogenetics on large trees. | 2017 | ent a new [R package], named c | |
| 29091996 | javascript | Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains. | 2017 | web-based [javascript] visualiza | |
| 29088314 | r | An exact test for comparing a fixed quantitative property between gene sets. | 2017 | ilable on [CRAN]. | |
| 29088309 | python | DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry. | 2017 | the [python] tool dieg | |
| 29088309 | perl | DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry. | 2017 | ython and [perl] parsers f | |
| 29087464 | python | MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks. | 2017 | mented in [python] and suppo | |
| 29087446 | r | ndexr-an R package to interface with the network data exchange. | 2018 | ndexr-an [R package] to interf | |
| 29087435 | javascript | Dynamic Assessment of Microbial Ecology (DAME): A web app for interactive analysis and visualization of microbial sequencing data. | 2017 | css, and [javascript]. it is fr | |
| 29077810 | python | ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. | 2017 | mented in [python] and relea | |
| 29077807 | r | pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. | 2017 | developed [Bioconductor] package f | |
| 29077797 | c++ | netReg: Network-regularized linear models for biological association studies. | 2017 | ckage and [C++] commandli | |
| 29077797 | r | netReg: Network-regularized linear models for biological association studies. | 2017 | tion. the [R package] is freely | |
| 29077795 | r | Group Spike-and-Slab Lasso Generalized Linear Models for Disease Prediction and Associated Genes Detection by Incorporating Pathway Information. | 2017 | available [R package] bhglm (ht | |
| 29077792 | r | Unsupervised multiple kernel learning for heterogeneous data integration. | 2017 | le in the [R package] mixkernel | |
| 29069317 | mathlab | Constructing Prediction Models from Expression Profiles for Large Scale lncRNA-miRNA Interaction Profiling. | 2017 | [matlab] codes and | |
| 29069312 | mathlab | PESTO: Parameter EStimation TOolbox. | 2018 | mathworks [matlab]. it offer | |
| 29069305 | r | heatmaply: an R package for creating interactive cluster heatmaps for online publishing. | 2017 | maply: an [R package] for creat | |
| 29061110 | mathlab | A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). | 2017 | mented in [matlab] (version | |
| 29048524 | python | Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. | 2018 | in c and [python], and supp | |
| 29048466 | python | PyBEL: a computational framework for Biological Expression Language. | 2018 | universal [python] code. its | |
| 29045591 | c | SAGE2: parallel human genome assembly. | 2018 | sage2 is [written in C] ++ and op | |
| 29040453 | mathlab | Detection of Sputum by Interpreting the Time-frequency Distribution of Respiratory Sound Signal Using Image Processing Techniques. | 2017 | the [matlab] codes and | |
| 29040451 | r | An omnibus test for differential distribution analysis of microbiome sequencing data. | 2018 | [R package] is availa | |
| 29040384 | mathlab | SELANSI: a toolbox for Simulation of Stochastic Gene Regulatory Networks. | 2017 | under the [matlab] environme | |
| 29037149 | r | chngpt: threshold regression model estimation and inference. | 2017 | the [R package] chngpt pr | |
| 29036584 | python | cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. | 2017 | liparm, a [python] program t | |
| 29036584 | r | cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. | 2017 | examples [and R] scripts a | |
| 29036562 | r | nandb-number and brightness in R with a novel automatic detrending algorithm. | 2017 | an [R package] for perfo | |
| 29036558 | python | MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. | 2017 | able as a [python] package ( | |
| 29036557 | python | Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. | 2017 | altab and [python] scripts a | |
| 29036546 | java | CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. | 2017 | mented in [java]. crocobla | |
| 29036536 | python | wft4galaxy: a workflow testing tool for galaxy. | 2017 | a regular [python] program o | |
| 29036513 | r | ScanGEO: parallel mining of high-throughput gene expression data. | 2017 | e code is [written in R] and imple | |
| 29036507 | r | ggseqlogo: a versatile R package for drawing sequence logos. | 2017 | versatile [R package] for drawi | |
| 29036452 | python | A nonparametric significance test for sampled networks. | 2018 | ritten in [python] and uses | |
| 29036400 | r | Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data. | 2017 | mpledrift [R package] is availa | |
| 29036359 | r | proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry. | 2017 | ble as an [R package] on the bi | |
| 29036320 | r | Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. | 2017 | ble as an [R package] at the cr | |
| 29036318 | r | DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. | 2018 | -friendly [R package] with a de | |
| 29036307 | mathlab | Irys Extract. | 2018 | eloped in [matlab] r2015a, i | |
| 29036291 | python | Phylotyper: in silico predictor of gene subtypes. | 2017 | yper is a [python] and r pac | |
| 29036291 | r | Phylotyper: in silico predictor of gene subtypes. | 2017 | ython and [R package]. it is av | |
| 29036287 | r | powsimR: power analysis for bulk and single cell RNA-seq experiments. | 2017 | the [R package] and assoc | |
| 29036277 | python | PySeqLab: an open source Python package for sequence labeling and segmentation. | 2017 | en source [python] package f | |
| 29029016 | r | diffuStats: an R package to compute diffusion-based scores on biological networks. | 2018 | stats: an [R package] to comput | |
| 29028963 | r | ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. | 2018 | matlab [and R] scripts u | |
| 29028963 | mathlab | ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. | 2018 | [matlab] and r scr | |
| 29028961 | r | Towards unified quality verification of synthetic count data with countsimQC. | 2018 | ted as an [R package] (for r ve | |
| 29028923 | r | Detecting presence of mutational signatures in cancer with confidence. | 2017 | ted in an [R package], called s | |
| 29028911 | r | Genome-wide pre-miRNA discovery from few labeled examples. | 2018 | an [R package] can be do | |
| 29028902 | python | graphkernels: R and Python packages for graph comparison. | 2018 | ls: r and [python] packages | |
| 29028896 | python | PyDREAM: high-dimensional parameter inference for biological models in python. | 2018 | models in [python]. | |
| 29028890 | r | MALDIrppa: quality control and robust analysis for mass spectrometry data. | 2018 | this [R package] helps to | |
| 29028267 | r | VariantTools: an extensible framework for developing and testing variant callers. | 2017 | ttp://www.[Bioconductor].org/. | |
| 29028264 | javascript | TeachEnG: a Teaching Engine for Genomics. | 2017 | ritten in [javascript] and compa | |
| 29028262 | r | TSIS: an R package to infer alternative splicing isoform switches for time-series data. | 2017 | tsis: an [R package] to infer | |
| 29028260 | r | pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. | 2017 | he pulser [R package] simplifie | |
| 29025394 | r | Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. | 2017 | ble as an [R package] from the | |
| 29017446 | python | LSTrAP: efficiently combining RNA sequencing data into co-expression networks. | 2017 | mented in [python] 3.4 (or h | |
| 28981576 | r | SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data. | 2017 | f segtool [R package] is freely | |
| 28981573 | r | OPATs: Omnibus P-value association tests. | 2017 | mmed in r [and R] graphical | |
| 28974199 | r | Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. | 2017 | an [R package] instantia | |
| 28968872 | python | PySCeSToolbox: a collection of metabolic pathway analysis tools. | 2018 | on to the [python] simulator | |
| 28968815 | mathlab | A Novel SCCA Approach via Truncated ℓ1-norm and Truncated Group Lasso for Brain Imaging Genetics. | 2017 | the [matlab] code and | |
| 28968783 | java | SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy. | 2018 | n imagej. [java] and cuda | |
| 28968706 | r | LinkageMapView - Rendering High Resolution Linkage and QTL Maps. | 2017 | n package [written in R] that prod | |
| 28968704 | r | SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. | 2017 | he matlab [and R] version o | |
| 28968704 | mathlab | SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. | 2017 | the [matlab] and r ver | |
| 28968701 | python | Interactive network visualization in Jupyter notebooks: visJS2jupyter. | 2018 | ps://pypi.[python].org/pypi/ | |
| 28968701 | javascript | Interactive network visualization in Jupyter notebooks: visJS2jupyter. | 2018 | uses the [javascript] library v | |
| 28968690 | r | regNet: An R package for network-based propagation of gene expression alterations. | 2017 | egnet: an [R package] for netwo | |
| 28968682 | r | Identification and visualization of differential isoform expression in RNA-seq time series. | 2018 | ty of the [R package] masigpro | |
| 28968671 | r | Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. | 2018 | ded in an [R package] freely av | |
| 28968667 | mathlab | Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm. | 2018 | mented by [matlab] and c ++. | |
| 28968663 | mathlab | Morphologically constrained and data informed cell segmentation of budding yeast. | 2018 | the [matlab] code for | |
| 28968645 | python | Kfits: a software framework for fitting and cleaning outliers in kinetic measurements. | 2018 | mented in [python] and avail | |
| 28968644 | r | Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics. | 2018 | lizer: an [R package] for norma | |
| 28968630 | r | Pathway enrichment analysis approach based on topological structure and updated annotation of pathway. | 2017 | eloped an [R package] to implem | |
| 28962546 | c++ | pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. | 2017 | language [C++]. furtherm | |
| 28962546 | r | pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. | 2017 | ulver: an [R package] for paral | |
| 28961999 | r | Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning. | 2017 | st-cases, [and R] scripts u | |
| 28961965 | java | Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. | 2017 | n japsa-a [java] tools kit | |
| 28961912 | r | Enabling reproducible real-time quantitative PCR research: the RDML package. | 2017 | computing [language r]. rdml is | |
| 28961895 | mathlab | HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation. | 2017 | the [matlab] code of t | |
| 28961861 | r | Conditional asymptotic inference for the kernel association test. | 2017 | ed in the [R package] igasso. | |
| 28961782 | c | MetaCache: context-aware classification of metagenomic reads using minhashing. | 2017 | software [written in C] ++ and ca | |
| 28961763 | r | psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes. | 2017 | net2r, an [R package] that cont | |
| 28961761 | r | clustComp, a bioconductor package for the comparison of clustering results. | 2017 | stcomp, a [Bioconductor] package f | |
| 28961756 | mathlab | 4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities. | 2018 | powerful [matlab] toolbox f | |
| 28961747 | r | An improved compound Poisson model for the number of motif hits in DNA sequences. | 2017 | able as a [Bioconductor] package n | |
| 28961746 | r | ChAMP: updated methylation analysis pipeline for Illumina BeadChips. | 2017 | on of the [Bioconductor] package c | |
| 28961742 | perl | BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data. | 2017 | mented in [perl] and runs | |
| 28961740 | python | EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing. | 2017 | s minimal [python] dependenc | |
| 28961706 | r | Genome-wide association studies using a penalized moving-window regression. | 2017 | ovided in [R package] mwlasso. | |
| 28961702 | r | MWASTools: an R/Bioconductor package for metabolome-wide association studies. | 2017 | ols is an [R package] designed | |
| 28957498 | r | ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data. | 2017 | nce is an [R package] available | |
| 28927242 | r | biospear: an R package for biomarker selection in penalized Cox regression. | 2018 | spear: an [R package] for bioma | |
| 28923005 | r | Methods for discovering genomic loci exhibiting complex patterns of differential methylation. | 2017 | egmentseq [R package] is extend | |
| 28911038 | perl | Spliceman2: a computational web server that predicts defects in pre-mRNA splicing. | 2017 | ache, and [perl], with all | |
| 28882003 | python | miniMDS: 3D structural inference from high-resolution Hi-C data. | 2017 | a [python] implement | |
| 28881993 | java | Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. | 2017 | ritten in [java] is availa | |
| 28881990 | r | A new method to study the change of miRNA-mRNA interactions due to environmental exposures. | 2017 | [R package] ijrf is a | |
| 28881987 | mathlab | Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems. | 2017 | nsight, a [matlab] script is | |
| 28881985 | mathlab | popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. | 2017 | he popfba [matlab] function | |
| 28881984 | mathlab | Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. | 2017 | the [matlab] code for | |
| 28881983 | mathlab | A scalable moment-closure approximation for large-scale biochemical reaction networks. | 2017 | en-source [matlab] toolbox c | |
| 28881979 | mathlab | Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis. | 2017 | the [matlab] code is a | |
| 28881975 | r | Molecular signatures that can be transferred across different omics platforms. | 2017 | lete data [and R] codes nec | |
| 28881967 | mathlab | HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape. | 2017 | the [matlab] implement | |
| 28750623 | r | l1kdeconv: an R package for peak calling analysis with LINCS L1000 data. | 2017 | econv: an [R package] for peak | |
| 28724417 | r | Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications. | 2017 | mediation [R package] enables t | |
| 28716000 | python | Quantiprot - a Python package for quantitative analysis of protein sequences. | 2017 | iprot - a [python] package f | |
| 28683752 | r | TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. | 2017 | nction in [R package] tnseq and | |
| 28676075 | r | sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. | 2017 | gnesr: an [R package] for simul | |
| 28673016 | mathlab | FALCON: a toolbox for the fast contextualization of logical networks. | 2017 | propose a [matlab] toolbox, | |
| 28666369 | r | CausalR: extracting mechanistic sense from genome scale data. | 2017 | able from [Bioconductor]. | |
| 28666322 | python | SVM-dependent pairwise HMM: an application to protein pairwise alignments. | 2017 | a [python] implement | |
| 28666320 | mathlab | Inferring transcriptional logic from multiple dynamic experiments. | 2017 | ritten in [matlab] and stati | |
| 28666314 | python | GPU-powered model analysis with PySB/cupSODA. | 2017 | from the [python] package i | |
| 28659129 | python | SLMSuite: a suite of algorithms for segmenting genomic profiles. | 2017 | e them in [python], ruby and | |
| 28659129 | c++ | SLMSuite: a suite of algorithms for segmenting genomic profiles. | 2017 | ruby and [C++]. slmsuite | |
| 28655158 | python | CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. | 2017 | ritten in [python] and avail | |
| 28655153 | r | The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. | 2017 | le as the [R package] kseaapp | |
| 28651569 | mathlab | ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. | 2017 | retros: a [matlab] toolbox f | |
| 28651334 | r | TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP-SNP interactions. | 2017 | d through [CRAN] and is av | |
| 28651329 | java | High-speed and high-ratio referential genome compression. | 2017 | c ++ and [java] source co | |
| 28645171 | r | UpSetR: an R package for the visualization of intersecting sets and their properties. | 2017 | psetr: an [R package] for the v | |
| 28645150 | python | GfaPy: a flexible and extensible software library for handling sequence graphs in Python. | 2017 | graphs in [python]. | |
| 28637232 | python | PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. | 2017 | ritten in [python3] and r und | |
| 28637232 | r | PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. | 2017 | n python3 [and R] under the | |
| 28637183 | python | NucliTrack: an integrated nuclei tracking application. | 2017 | en source [python] package. | |
| 28637183 | mathlab | NucliTrack: an integrated nuclei tracking application. | 2017 | itrack. a [matlab] toolbox i | |
| 28633423 | r | rqt: an R package for gene-level meta-analysis. | 2017 | rqt: an [R package] for gene- | |
| 28633418 | r | Detecting and removing multiplicative spatial bias in high-throughput screening technologies. | 2017 | ilable on [CRAN]. | |
| 28633357 | r | matter: an R package for rapid prototyping with larger-than-memory datasets on disk. | 2017 | atter: an [R package] for rapid | |
| 28633344 | java | Pheno4J: a gene to phenotype graph database. | 2017 | data. our [java] based sol | |
| 28633344 | python | Pheno4J: a gene to phenotype graph database. | 2017 | java and [python] code are | |
| 28617225 | c++ | A greedy alignment-free distance estimator for phylogenetic inference. | 2017 | mented in [C++] and has b | |
| 28605539 | python | runBNG: a software package for BioNano genomic analysis on the command line. | 2017 | perl and [python] software. | |
| 28605539 | bash | runBNG: a software package for BioNano genomic analysis on the command line. | 2017 | ritten in [bash], with the | |
| 28605539 | perl | runBNG: a software package for BioNano genomic analysis on the command line. | 2017 | ges, gcc, [perl] and pytho | |
| 28605519 | r | CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization. | 2017 | types, an [R package] for ident | |
| 28605449 | python | FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. | 2017 | mented in [python] 3 and jav | |
| 28605449 | javascript | FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. | 2017 | hon 3 and [javascript], and is m | |
| 28595310 | r | Phantom: investigating heterogeneous gene sets in time-course data. | 2017 | phantom . [R package] of phanto | |
| 28587596 | r | A systematic evaluation of nucleotide properties for CRISPR sgRNA design. | 2017 | iency. an [R package] predictsg | |
| 28582565 | python | ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. | 2017 | from the [python] package i | |
| 28582538 | python | BreakPoint Surveyor: a pipeline for structural variant visualization. | 2017 | ted in r, [python] and bash | |
| 28582538 | bash | BreakPoint Surveyor: a pipeline for structural variant visualization. | 2017 | ython and [bash] scripts, | |
| 28582485 | python | COMPASS: the COMPletely Arbitrary Sequence Simulator. | 2017 | mented in [python] 2.7, and | |
| 28582481 | python | FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation. | 2017 | ritten in [python] script an | |
| 28575207 | python | Moran's I quantifies spatio-temporal pattern formation in neural imaging data. | 2017 | [python] 2.7 code | |
| 28575171 | r | karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. | 2017 | e through [Bioconductor] (http://w | |
| 28575169 | python | MD-TASK: a software suite for analyzing molecular dynamics trajectories. | 2017 | mented in [python] and suppo | |
| 28558647 | c++ | Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. | 2017 | mented in [C++], hapl-o-m | |
| 28549446 | java | gnparser : a powerful parser for scientific names based on Parsing Expression Grammar. | 2017 | . it is a [java] tool writ | |
| 28545397 | java | JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. | 2017 | jed: a [java] essential | |
| 28545397 | r | JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. | 2017 | sion of q [and R], and repo | |
| 28535748 | r | DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data. | 2017 | datasets [and R] packages | |
| 28535188 | r | Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. | 2017 | as the [Bioconductor] package n | |
| 28532394 | python | CircularLogo: A lightweight web application to visualize intra-motif dependencies. | 2017 | cript and [python] based on | |
| 28532394 | javascript | CircularLogo: A lightweight web application to visualize intra-motif dependencies. | 2017 | mented in [javascript] and pytho | |
| 28525538 | r | chimeraviz: a tool for visualizing chimeric RNA. | 2017 | viz is an [R package] available | |
| 28525531 | javascript | PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. | 2017 | using the [javascript] library d | |
| 28521770 | python | Coordinates and intervals in graph-based reference genomes. | 2017 | ve made a [python] package f | |
| 28520900 | mathlab | Accelerating high-dimensional clustering with lossless data reduction. | 2017 | r, [matlab] and sas/i | |
| 28520848 | mathlab | Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. | 2017 | nted as a [matlab] package, | |
| 28505270 | r | HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens. | 2017 | en-source [R package], download | |
| 28505251 | r | False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing. | 2017 | [R package] structfdr | |
| 28505247 | r | Single-cell regulome data analysis by SCRAT. | 2017 | rat as an [R package]. | |
| 28505226 | java | OMTools: a software package for visualizing and processing optical mapping data. | 2017 | mented in [java] 1.8 and r | |
| 28499413 | mathlab | Ranking metrics in gene set enrichment analysis: do they matter? | 2017 | mented in [matlab], and is a | |
| 28498885 | python | PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics. | 2017 | mented in [python], and supp | |
| 28494801 | mathlab | Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order. | 2017 | present a [matlab] spectral | |
| 28481978 | r | Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. | 2017 | [R package] and sourc | |
| 28481966 | r | RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. | 2017 | efactored [Bioconductor] package f | |
| 28475668 | java | MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud. | 2017 | ritten in [java] to maximi | |
| 28475666 | r | Assembling draft genomes using contiBAIT. | 2017 | ilable on [Bioconductor]. source f | |
| 28475662 | r | twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. | 2017 | en source [R package] 'twoddpcr | |
| 28472919 | javascript | WebGIVI: a web-based gene enrichment analysis and visualization tool. | 2017 | document [javascript] libraries | |
| 28472395 | mathlab | SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer. | 2017 | inchet: a [matlab] toolbox f | |
| 28472345 | python | STOPGAP: a database for systematic target opportunity assessment by genetic association predictions. | 2017 | perl and [python] scripts a | |
| 28472345 | perl | STOPGAP: a database for systematic target opportunity assessment by genetic association predictions. | 2017 | shell, r, [perl] and pytho | |
| 28472273 | r | EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons. | 2017 | an [R package] implement | |
| 28472272 | python | modlAMP: Python for antimicrobial peptides. | 2017 | modlamp: [python] for antim | |
| 28472271 | r | Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. | 2017 | mented in [R language] and matla | |
| 28472271 | mathlab | Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. | 2017 | guage and [matlab]. | |
| 28472248 | r | Accounting for tumor purity improves cancer subtype classification from DNA methylation data. | 2017 | s part of [R package] infiniump | |
| 28472230 | python | OMSim: a simulator for optical map data. | 2017 | the [python] simulatio | |
| 28472220 | r | The spike-and-slab lasso Cox model for survival prediction and associated genes detection. | 2017 | available [R package] bhglm ( h | |
| 28464826 | java | microTaboo: a general and practical solution to the k-disjoint problem. | 2017 | , running [java] 7 and hig | |
| 28464823 | r | Zipper plot: visualizing transcriptional activity of genomic regions. | 2017 | ogramming [language r] and is fr | |
| 28453684 | python | MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. | 2017 | eloped in [python], using r | |
| 28453684 | r | MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. | 2017 | n python, [using R] for data | |
| 28453675 | javascript | CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files. | 2017 | mented in [javascript] and is av | |
| 28453674 | c | ntCard: a streaming algorithm for cardinality estimation in genomics data. | 2017 | ntcard is [written in C] ++ and is | |
| 28453672 | python | Primerize-2D: automated primer design for RNA multidimensional chemical mapping. | 2017 | and-alone [python] package f | |
| 28453670 | r | GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. | 2017 | en source [R package] that gene | |
| 28453611 | r | modSaRa: a computationally efficient R package for CNV identification. | 2017 | efficient [R package] for cnv i | |
| 28449031 | python | RNAblueprint: flexible multiple target nucleic acid sequence design. | 2017 | ritten in [python] to demons | |
| 28444139 | mathlab | Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound. | 2017 | the [matlab] code for | |
| 28444126 | r | CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. | 2017 | uses the [R package] drc for a | |
| 28431087 | mathlab | A method for learning a sparse classifier in the presence of missing data for high-dimensional biological datasets. | 2017 | a [matlab] implement | |
| 28430977 | java | Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. | 2017 | eloped in [java] and it is | |
| 28420344 | python | Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. | 2017 | (jqmm): a [python] library f | |
| 28419235 | r | A Bayesian group sparse multi-task regression model for imaging genetics. | 2017 | ble as an [R package] 'bgsmtr' | |
| 28410574 | r | Comparison of different cell type correction methods for genome-scale epigenetics studies. | 2017 | the minfi [R package], the meth | |
| 28407035 | javascript | IcyTree: rapid browser-based visualization for phylogenetic trees and networks. | 2017 | ient-side [javascript] (no plugi | |
| 28407034 | r | Network module-based model in the differential expression analysis for RNA-seq. | 2017 | the [R package] seqmade i | |
| 28402395 | python | mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. | 2017 | a set of [python] packages | |
| 28402393 | r | MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data. | 2017 | en-source [R language], together | |
| 28398543 | r | FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. | 2017 | from the [Bioconductor] website ( | |
| 28398503 | r | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc. | 2017 | eegc [R package] is releas | |
| 28398502 | python | PyGOLD: a python based API for docking based virtual screening workflow generation. | 2017 | pygold: a [python] based api | |
| 28398468 | r | RTK: efficient rarefaction analysis of large datasets. | 2017 | c ++ [and R] source co | |
| 28398456 | java | GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. | 2017 | ritten in [java]. it is fr | |
| 28388874 | python | Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. | 2017 | ompatible [python] package a | |
| 28383704 | python | ploidyNGS: visually exploring ploidy with Next Generation Sequencing data. | 2017 | mented in [python] and r. | |
| 28383704 | r | ploidyNGS: visually exploring ploidy with Next Generation Sequencing data. | 2017 | in python [and R]. | |
| 28381205 | python | The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. | 2017 | (jqmm): a [python] library f | |
| 28379466 | python | Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models. | 2017 | ckinac, a [python] package t | |
| 28379351 | java | SQC: secure quality control for meta-analysis of genome-wide association studies. | 2017 | mented in [java] and is pu | |
| 28379302 | r | cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data. | 2017 | s450k: an [R package] for compa | |
| 28369371 | perl | EUPAN enables pan-genome studies of a large number of eukaryotic genomes. | 2017 | mented in [perl], r and c | |
| 28369339 | python | HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. | 2017 | julia and [python], and deta | |
| 28369316 | r | annotatr: genomic regions in context. | 2017 | annotatr [Bioconductor] package t | |
| 28369284 | python | Spresso: an ultrafast compound pre-screening method based on compound decomposition. | 2017 | c ++ and [python], and is a | |
| 28369284 | c | Spresso: an ultrafast compound pre-screening method based on compound decomposition. | 2017 | presso is [written in C] ++ and py | |
| 28369277 | r | GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. | 2017 | tps://www.[Bioconductor].org/packa | |
| 28369256 | mathlab | Entropy-based consensus clustering for patient stratification. | 2017 | the [matlab] package i | |
| 28369250 | r | rMSI: an R package for MS imaging data handling and visualization. | 2017 | rmsi: an [R package] for ms im | |
| 28369225 | java | Aozan: an automated post-sequencing data-processing pipeline. | 2017 | mented in [java] and pytho | |
| 28369225 | python | Aozan: an automated post-sequencing data-processing pipeline. | 2017 | java and [python], supporte | |
| 28369222 | r | EthSEQ: ethnicity annotation from whole exome sequencing data. | 2017 | [R package] available | |
| 28369214 | java | Constructing linkage maps in the genomics era with MapDisto 2.0. | 2017 | on of new [java] modules t | |
| 28369193 | mathlab | Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming. | 2017 | mented in [matlab], and is p | |
| 28369168 | python | ConKit: a python interface to contact predictions. | 2017 | conkit: a [python] interface | |
| 28369166 | python | Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues. | 2017 | mented in [python] and freel | |
| 28361684 | r | NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis. | 2017 | ender: an [R package] for funct | |
| 28361683 | mathlab | Comparative network stratification analysis for identifying functional interpretable network biomarkers. | 2017 | nted as a [matlab] package, | |
| 28340552 | python | StrAuto: automation and parallelization of STRUCTURE analysis. | 2017 | e popular [python] program s | |
| 28334409 | r | SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. | 2017 | ns) is an [R package] to simula | |
| 28334395 | r | poRe GUIs for parallel and real-time processing of MinION sequence data. | 2017 | s for the [R package] pore that | |
| 28334390 | r | SeqArray-a storage-efficient high-performance data format for WGS variant calls. | 2017 | ttp://www.[Bioconductor].org/packa | |
| 28334360 | python | HLA-MA: simple yet powerful matching of samples using HLA typing results. | 2017 | mented in [python] 3 and fre | |
| 28334349 | r | DeepBlueR: large-scale epigenomic analysis in R. | 2017 | is in the [Bioconductor] ecosystem | |
| 28334344 | r | Estimating gene regulatory networks with pandaR. | 2017 | conductor [R package] and is av | |
| 28334340 | r | Meta-analytic framework for liquid association. | 2017 | a metala [R package], data and | |
| 28334306 | java | PeptideMapper: efficient and versatile amino acid sequence and tag mapping. | 2017 | en source [java] compomics | |
| 28334266 | python | Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data. | 2017 | ted using [python], mongodb, | |
| 28334266 | bash | Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data. | 2017 | d various [bash] shell scr | |
| 28334231 | javascript | ProtVista: visualization of protein sequence annotations. | 2017 | ista is a [javascript] component | |
| 28334222 | r | QRank: a novel quantile regression tool for eQTL discovery. | 2017 | an [R package] is availa | |
| 28334215 | mathlab | Systematic inference of functional phosphorylation events in yeast metabolism. | 2017 | [matlab] codes for | |
| 28334199 | mathlab | Stepwise inference of likely dynamic flux distributions from metabolic time series data. | 2017 | mented in [matlab] (version | |
| 28334194 | python | swga: a primer design toolkit for selective whole genome amplification. | 2017 | mented in [python] and c and | |
| 28334167 | r | Identification of genetic outliers due to sub-structure and cryptic relationships. | 2017 | le in the [R package] stego fro | |
| 28334165 | r | ctsGE-clustering subgroups of expression data. | 2017 | rt of the [Bioconductor] project a | |
| 28334101 | mathlab | RefBool: a reference-based algorithm for discretizing gene expression data. | 2017 | ilable as [matlab] files in | |
| 28334094 | r | FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. | 2017 | mented in [R package] funnel, f | |
| 28327092 | r | metaX: a flexible and comprehensive software for processing metabolomics data. | 2017 | eloped an [R package], metax, t | |
| 28302053 | python | A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. | 2017 | efficient [python] library f | |
| 28302053 | javascript | A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. | 2017 | quivalent [javascript] object no | |
| 28302051 | c++ | microclass: an R-package for 16S taxonomy classification. | 2017 | mented in [C++] but opera | |
| 28302051 | r | microclass: an R-package for 16S taxonomy classification. | 2017 | resent an [R package] with tool | |
| 28284194 | java | ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface. | 2017 | opment in [java] and r is | |
| 28284194 | r | ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface. | 2017 | wraps the [R package] tcr and f | |
| 28264647 | r | The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. | 2017 | ted as an [R package], and is a | |
| 28259147 | r | ProteoModlR for functional proteomic analysis. | 2017 | and-alone [R package]. | |
| 28259142 | r | Avoiding the pitfalls of gene set enrichment analysis with SetRank. | 2017 | ble as an [R package] and throu | |
| 28253840 | r | Model based heritability scores for high-throughput sequencing data. | 2017 | ed in the [R package] heritseq. | |
| 28253836 | r | flippant-An R package for the automated analysis of fluorescence-based scramblase assays. | 2017 | ippant-an [R package] for the a | |
| 28241739 | r | MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. | 2017 | ixomics r [CRAN] package, | |
| 28241736 | r | BBCAnalyzer: a visual approach to facilitate variant calling. | 2017 | call. the [R package] is freely | |
| 28231764 | r | stpm: an R package for stochastic process model. | 2017 | stpm: an [R package] for stoch | |
| 28231760 | c++ | Meta-aligner: long-read alignment based on genome statistics. | 2017 | mented in [C++] and runs | |
| 28209127 | r | repo: an R package for data-centered management of bioinformatic pipelines. | 2017 | repo: an [R package] for data- | |
| 28205676 | c | GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification. | 2017 | garlic is [written in C] ++. sourc | |
| 28203714 | r | Glimma: interactive graphics for gene expression analysis. | 2017 | he glimma [R package] is availa | |
| 28203707 | r | Correlated mutations select misfolded from properly folded proteins. | 2017 | he decoys ['R'] us databa | |
| 28203700 | r | Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. | 2017 | ble as an [R package] at: http: | |
| 28200075 | r | An approach to infer putative disease-specific mechanisms using neighboring gene networks. | 2017 | able an a [Bioconductor] package. | |
| 28200073 | mathlab | AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs. | 2017 | the [matlab] code is a | |
| 28200033 | r | Genome-wide genetic heterogeneity discovery with categorical covariates. | 2017 | an [R package] fastcmh i | |
| 28187713 | mathlab | Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. | 2017 | ram using [matlab] r2014a un | |
| 28186257 | r | sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets. | 2017 | sfinx: an [R package] for the e | |
| 28186227 | r | OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations. | 2017 | able from [Bioconductor] for linux | |
| 28186226 | python | Binning_refiner: improving genome bins through the combination of different binning programs. | 2017 | mented in [python3] and is fr | |
| 28186225 | r | VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics. | 2017 | this, an [R package] (valorate | |
| 28186221 | bash | Kollector: transcript-informed, targeted de novo assembly of gene loci. | 2017 | nted as a [bash] script, a | |
| 28185580 | python | On the consistency of orthology relationships. | 2016 | mented in [python] and is av | |
| 28185573 | python | RGmatch: matching genomic regions to proximal genes in omics data integration. | 2016 | sy-to-use [python] tool that | |
| 28185568 | r | Identification of expression patterns in the progression of disease stages by integration of transcriptomic data. | 2016 | re script [written in R], named ge | |
| 28185544 | python | PWHATSHAP: efficient haplotyping for future generation sequencing. | 2016 | eloped in [python] and suppo | |
| 28177067 | python | GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data. | 2017 | requires [python] 2.7 and s | |
| 28177064 | perl | CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data. | 2017 | in php + [perl] + r and c | |
| 28174903 | c | Phyx: phylogenetic tools for unix. | 2017 | programs [written in C] ++ to exp | |
| 28174896 | r | PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. | 2017 | he cogaps [Bioconductor] package ( | |
| 28174895 | r | cooccurNet: an R package for co-occurrence network construction and analysis. | 2017 | urnet: an [R package] for co-oc | |
| 28172632 | r | SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data. | 2017 | alyzer is [written in R], is platf | |
| 28172529 | python | Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. | 2017 | cplots: a [python] package f | |
| 28172469 | r | QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. | 2017 | qubic: a [Bioconductor] package f | |
| 28172448 | java | OMBlast: alignment tool for optical mapping using a seed-and-extend approach. | 2017 | ented for [java] 1.7 and i | |
| 28172447 | r | Powerful differential expression analysis incorporating network topology for next-generation sequencing data. | 2017 | ted in an [R package] pathdeseq | |
| 28172414 | r | simPATHy: a new method for simulating data from perturbed biological PATHways. | 2017 | thy is an [R package], it is op | |
| 28166716 | python | PyHLA: tests for the association between HLA alleles and diseases. | 2017 | veloped a [python] package c | |
| 28165116 | r | pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. | 2017 | the [R package] 'petm' is | |
| 28165111 | python | MotifNet: a web-server for network motif analysis. | 2017 | mented in [python] with data | |
| 28165109 | python | cyvcf2: fast, flexible variant analysis with Python. | 2017 | ysis with [python]. | |
| 28158604 | python | Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. | 2017 | eloped in [python], making u | |
| 28158442 | python | Automated cell type discovery and classification through knowledge transfer. | 2017 | a [python] package ( | |
| 28158396 | r | FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions. | 2017 | d fit, an [R package] that offe | |
| 28158333 | r | admixturegraph: an R package for admixture graph manipulation and fitting. | 2017 | graph: an [R package] for admix | |
| 28152980 | r | DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD. | 2017 | d in perl [and R] under the | |
| 28152980 | perl | DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD. | 2017 | mented in [perl] and r und | |
| 28130242 | r | Hierarchical sets: analyzing pangenome structure through scalable set visualizations. | 2017 | hicalsets [R package] available | |
| 28130241 | r | Classification of RNA structure change by 'gazing' at experimental data. | 2017 | asssnitch [R package] is freely | |
| 28130233 | python | A comprehensive quality control workflow for paired tumor-normal NGS experiments. | 2017 | requires [python] 2.7 and m | |
| 28130232 | r | ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing. | 2017 | tware and [R package] from bioc | |
| 28130227 | java | Unrealistic phylogenetic trees may improve phylogenetic footprinting. | 2017 | mented in [java] and can b | |
| 28119308 | r | QCEWAS: automated quality control of results of epigenome-wide association studies. | 2017 | he qcewas [R package]. qcewas e | |
| 28119307 | java | ASCIIGenome: a command line genome browser for console terminals. | 2017 | ritten in [java]. conseque | |
| 28118818 | r | GSAR: Bioconductor package for Gene Set analysis in R. | 2017 | gsar: [Bioconductor] package f | |
| 28114896 | java | Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. | 2017 | eloped in [java], authors | |
| 28110292 | r | Biomartr: genomic data retrieval with R. | 2017 | en source [R package], biomartr | |
| 28108449 | mathlab | Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data. | 2017 | mented in [matlab]. | |
| 28105912 | python | DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks. | 2016 | en source [python] package. | |
| 28096085 | perl | Improved orthology inference with Hieranoid 2. | 2017 | [perl] code free | |
| 28096075 | r | hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. | 2017 | dual perl [and R] scripts, | |
| 28096075 | perl | hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. | 2017 | ndividual [perl] and r scr | |
| 28095799 | r | MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. | 2017 | taset: an [R package] for encap | |
| 28093409 | python | DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics. | 2017 | eadme for [python] 2 and 3 v | |
| 28088763 | r | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. | 2017 | e through [Bioconductor] at http:/ | |
| 28088185 | r | iGC-an integrated analysis package of gene expression and copy number alteration. | 2017 | tps://www.[Bioconductor].org/packa | |
| 28088176 | r | TTCA: an R package for the identification of differentially expressed genes in time course microarray data. | 2017 | ttca: an [R package] for the i | |
| 28073760 | r | Better diagnostic signatures from RNAseq data through use of auxiliary co-data. | 2017 | dge is an [R package] that incl | |
| 28073756 | r | Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires. | 2017 | tor . the [R package] e1071 is | |
| 28073755 | r | Advanced Boolean modeling of biological networks applied to systems pharmacology. | 2017 | ent on r) [R package]. the resu | |
| 28069594 | r | SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network. | 2017 | an [R package] sigmod is | |
| 28065917 | r | Transformation and model choice for RNA-seq co-expression analysis. | 2017 | propose a [Bioconductor] package c | |
| 28065903 | python | caspo: a toolbox for automated reasoning on the response of logical signaling networks families. | 2017 | oolbox, a [python] package i | |
| 28065901 | java | RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination. | 2017 | mented in [java], and is f | |
| 28065897 | mathlab | TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data. | 2017 | mented in [matlab] software | |
| 28065895 | java | Automated neuron tracing using probability hypothesis density filtering. | 2017 | en in the [java] programmi | |
| 28062444 | mathlab | Robust parameter estimation for dynamical systems from outlier-corrupted data. | 2017 | the [matlab] implement | |
| 28062443 | r | A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm. | 2017 | n 'pbcmc' [R package] at biocon | |
| 28062442 | perl | SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets. | 2017 | mented in [perl] and suppo | |
| 28061750 | java | GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. | 2017 | tandalone [java] applicati | |
| 28057685 | r | RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. | 2017 | platform [Bioconductor], to ensur | |
| 28057682 | perl | phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics. | 2017 | eton is a [perl] module an | |
| 28057677 | r | PanViz: interactive visualization of the structure of functionally annotated pangenomes. | 2017 | companion [R package] that faci | |
| 28057677 | javascript | PanViz: interactive visualization of the structure of functionally annotated pangenomes. | 2017 | tirely in [javascript] and is av | |
| 28056760 | perl | MPD: multiplex primer design for next-generation targeted sequencing. | 2017 | g the mpd [perl] package p | |
| 28056760 | javascript | MPD: multiplex primer design for next-generation targeted sequencing. | 2017 | rimers. a [javascript] web appli | |
| 28052927 | r | DNABarcodes: an R package for the systematic construction of DNA sample tags. | 2017 | codes: an [R package] for the s | |
| 28049409 | r | Negative binomial mixed models for analyzing microbiome count data. | 2017 | available [R package] bhglm ( h | |
| 28040696 | mathlab | Parameter estimation for dynamical systems with discrete events and logical operations. | 2017 | advanced [matlab] interface | |
| 28039164 | java | AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs. | 2017 | eloped in [java] 1.8 using | |
| 28035030 | java | CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. | 2017 | mented in [java] and the p | |
| 28035029 | r | geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation. | 2017 | ution, an [R package] that assi | |
| 28035026 | java | InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. | 2017 | esent the [java] applicati | |
| 28035024 | r | Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. | 2017 | from the [Bioconductor] project. | |
| 28031185 | r | MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer. | 2017 | [R package] 'metadcn' | |
| 28031184 | perl | SVScore: an impact prediction tool for structural variation. | 2017 | mented in [perl] and avail | |
| 28025202 | java | Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. | 2017 | rammed in [java], perl and | |
| 28025202 | r | Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. | 2017 | ava, perl [and R] and the s | |
| 28025202 | perl | Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. | 2017 | in java, [perl] and r and | |
| 28025197 | mathlab | A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases. | 2017 | [matlab] codes and | |
| 28025179 | r | Measuring the diversity of the human microbiota with targeted next-generation sequencing. | 2016 | ilable an [R package], diversit | |
| 28011790 | perl | High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. | 2017 | c ++ and [perl] and is av | |
| 28011789 | perl | myGenomeBrowser: building and sharing your own genome browser. | 2017 | mented in [perl], javascri | |
| 28011789 | javascript | myGenomeBrowser: building and sharing your own genome browser. | 2017 | in perl, [javascript], apache a | |
| 28011787 | r | switchde: inference of switch-like differential expression along single-cell trajectories. | 2017 | ompanying [R package] for ident | |
| 28011779 | r | cerebroViz: an R package for anatomical visualization of spatiotemporal brain data. | 2017 | roviz: an [R package] for anato | |
| 28011775 | r | MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. | 2017 | nal is an [R package] that allo | |
| 28011774 | python | Fast motif matching revisited: high-order PWMs, SNPs and indels. | 2017 | 0 and the [biopython] license ( | |
| 28011773 | r | ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. | 2017 | ents), an [R package] and assoc | |
| 28011770 | python | Simulation-based estimation of branching models for LTR retrotransposons. | 2017 | ted using [python] software. | |
| 28007037 | python | Block network mapping approach to quantitative trait locus analysis. | 2016 | mapping. [python] scripts a | |
| 28003266 | python | GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments. | 2017 | mented in [python], designed | |
| 28003264 | r | A general framework for association analysis of microbial communities on a taxonomic tree. | 2017 | relevant [R package] milineage | |
| 28003263 | r | bnstruct: an R package for Bayesian Network structure learning in the presence of missing data. | 2017 | truct: an [R package] for bayes | |
| 27998935 | r | CymeR: cytometry analysis using KNIME, docker and R. | 2017 | e, docker [and R]. | |
| 27998275 | r | Efficient randomization of biological networks while preserving functional characterization of individual nodes. | 2016 | en-source [Bioconductor] package e | |
| 27993789 | r | SPADEVizR: an R package for visualization, analysis and integration of SPADE results. | 2017 | evizr: an [R package] for visua | |
| 27993788 | java | MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework. | 2017 | mented in [java]. the sour | |
| 27993787 | bash | Improved VCF normalization for accurate VCF comparison. | 2017 | ban linux [bash] script al | |
| 27993786 | python | DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. | 2017 | [python] code avai | |
| 27993779 | java | Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. | 2017 | er/ . the [java] code file | |
| 27993778 | r | LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering. | 2017 | [R package] leap avai | |
| 27993774 | r | KODAMA: an R package for knowledge discovery and data mining. | 2017 | odama: an [R package] for knowl | |
| 27993773 | r | EGAD: ultra-fast functional analysis of gene networks. | 2017 | from the [Bioconductor] web site | |
| 27993773 | mathlab | EGAD: ultra-fast functional analysis of gene networks. | 2017 | in r and [matlab]. the pack | |
| 27964719 | javascript | Pathway collages: personalized multi-pathway diagrams. | 2016 | sent to a [javascript] pathway c | |
| 27938331 | r | Robust multi-group gene set analysis with few replicates. | 2016 | nsive. an [R package] implement | |
| 27938328 | perl | Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms. | 2016 | a simple [perl] script) w | |
| 27927171 | r | Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines. | 2016 | ons as an [R package] called bm | |
| 27923364 | r | PCAN: phenotype consensus analysis to support disease-gene association. | 2016 | ity as an [R package] ( http:// | |
| 27905885 | python | MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. | 2016 | mented in [python] and the s | |
| 27884103 | python | ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons. | 2016 | ritten in [python] language | |
| 27832739 | c++ | libFLASM: a software library for fixed-length approximate string matching. | 2016 | en-source [C++] software | |
| 27814681 | mathlab | WUFlux: an open-source platform for13C metabolic flux analysis of bacterial metabolism. | 2016 | nment) in [matlab], we built | |
| 27809781 | mathlab | PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. | 2016 | ide cnvs. [matlab] programs | |
| 27797784 | mathlab | BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods. | 2017 | [matlab] open sour | |
| 27797783 | python | PyBoolNet: a python package for the generation, analysis and visualization of boolean networks. | 2017 | oolnet: a [python] package f | |
| 27797782 | java | ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability. | 2017 | ghtweight [java] library f | |
| 27797782 | mathlab | ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability. | 2017 | y between [matlab] and image | |
| 27797781 | r | tcpl: the ToxCast pipeline for high-throughput screening data. | 2017 | the tcpl [R package] and its a | |
| 27797779 | java | JADOPPT: java based AutoDock preparing and processing tool. | 2017 | jadoppt: [java] based aut | |
| 27797778 | r | Network-based analysis of omics data: the LEAN method. | 2017 | ilable on [CRAN] ( https:/ | |
| 27797777 | python | INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. | 2017 | c ++ and [python]. full sou | |
| 27797775 | r | Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. | 2017 | unk-db/ , [R package] to comput | |
| 27797772 | r | ImpulseDE: detection of differentially expressed genes in time series data using impulse models. | 2017 | ede is an [R package] suited to | |
| 27797771 | r | Imputing gene expression to maximize platform compatibility. | 2017 | able as a [R package] (affyimpu | |
| 27797767 | r | miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions. | 2017 | conductor [R package] and web i | |
| 27797766 | python | yMap: an automated method to map yeast variants to protein modifications and functional regions. | 2017 | present a [python] framework | |
| 27797763 | python | Rabifier2: an improved bioinformatic classifier of Rab GTPases. | 2017 | from the [python] package i | |
| 27797762 | perl | CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. | 2017 | mented in [perl]. the sour | |
| 27797761 | javascript | Isomorphic semantic mapping of variant call format (VCF2RDF). | 2017 | mented in [javascript], and was | |
| 27797760 | r | Improving cross-study prediction through addon batch effect adjustment or addon normalization. | 2017 | ed in our [R package] bapred. | |
| 27797758 | r | gsrc: an R package for genome structure rearrangement calling. | 2017 | gsrc: an [R package] for genom | |
| 27794558 | r | Efficient detection of differentially methylated regions using DiMmeR. | 2017 | ogramming [language r], have no | |
| 27794557 | python | FractBias: a graphical tool for assessing fractionation bias following polyploidy. | 2017 | able with [python] 2.7 or ip | |
| 27667792 | r | Detecting subnetwork-level dynamic correlations. | 2017 | the [R package] is availa | |
| 27591080 | r | signeR: an empirical Bayesian approach to mutational signature discovery. | 2017 | able as a [R package] at http:/ | |
| 27793083 | python | MEvoLib v1.0: the first molecular evolution library for Python. | 2016 | brary for [python]. | |
| 27402908 | mathlab | SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. | 2016 | e popular [matlab] computati | |
| 27402905 | python | PyPanda: a Python package for gene regulatory network reconstruction. | 2016 | ypanda: a [python] package f | |
| 27402900 | r | samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. | 2016 | roduce an [R package] called sa | |
| 27378304 | r | MetaCycle: an integrated R package to evaluate periodicity in large scale data. | 2016 | ntegrated [R package] to evalua | |
| 27378300 | r | An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data. | 2016 | ed in the [R package] ebgenotyp | |
| 27378295 | mathlab | Unbiased classification of spatial strategies in the Barnes maze. | 2016 | nlab as a [matlab] applicati | |
| 27378292 | java | ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes. | 2016 | mented in [java], perl and | |
| 27378292 | perl | ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes. | 2016 | in java, [perl] and shell | |
| 27378290 | r | TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials. | 2016 | seind: an [R package] for estim | |
| 27784265 | r | AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments. | 2016 | -tool and [R package] for stati | |
| 27769170 | r | dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data. | 2016 | pradar: a [Bioconductor] package f | |
| 27766961 | python | VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. | 2016 | n c++ and [python], for read | |
| 27766961 | c++ | VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. | 2016 | ritten in [C++] and pytho | |
| 27766949 | r | Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold. | 2016 | ovide the [R package], lrcde, w | |
| 27766934 | r | CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints. | 2016 | the [R package] ccpromise | |
| 27760515 | perl | Convert your favorite protein modeling program into a mutation predictor: MODICT . | 2016 | he modict [perl] package a | |
| 27756200 | r | Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. | 2016 | ithm in a [Bioconductor] package t | |
| 27742697 | python | Visualizing the geography of genetic variants. | 2017 | q_api/ ). [python] and javas | |
| 27742697 | javascript | Visualizing the geography of genetic variants. | 2017 | ython and [javascript] source co | |
| 27733121 | r | Extending digital PCR analysis by modelling quantification cycle data. | 2016 | en source [language r] has been | |
| 27717304 | java | Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. | 2016 | mented in [java] and uses | |
| 27716034 | r | VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams. | 2016 | nndiagram [R package]. venndiag | |
| 27694195 | r | Combining multiple tools outperforms individual methods in gene set enrichment analyses. | 2017 | ble as an [R package] at http:/ | |
| 27677958 | r | Rare variant association test in family-based sequencing studies. | 2017 | ted in an [R package] 'gskat', | |
| 27667791 | java | LongISLND: in silico sequencing of lengthy and noisy datatypes. | 2016 | mented in [java] and avail | |
| 27667790 | java | cMapper: gene-centric connectivity mapper for EBI-RDF platform. | 2017 | ped using [java] and deplo | |
| 27663497 | perl | AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks. | 2017 | ork) is a [perl] applicati | |
| 27659774 | javascript | MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. | 2016 | on the d3 [javascript] library: | |
| 27659451 | r | PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. | 2017 | an [R package] of pssv i | |
| 27651481 | r | AlloMap6: an R package for genetic linkage analysis in allohexaploids. | 2017 | omap6: an [R package] for genet | |
| 27650223 | r | systemPipeR: NGS workflow and report generation environment. | 2016 | tems from [Bioconductor] ( http:// | |
| 27634949 | perl | Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. | 2017 | d in php, [perl], mysql, j | |
| 27634949 | javascript | Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes. | 2017 | l, mysql, [javascript], html and | |
| 27634947 | r | IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes. | 2017 | lling: an [R package] for the a | |
| 27634135 | python | Development of a prediction system for tail-anchored proteins. | 2016 | ritten in [python] is availa | |
| 27618863 | python | Tissue enrichment analysis for C. elegans genomics. | 2016 | ded using [python]'s standar | |
| 27616707 | mathlab | DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. | 2017 | a [matlab] package o | |
| 27614350 | java | Assessment of cancer and virus antigens for cross-reactivity in human tissues. | 2017 | nted as a [java] program, | |
| 27605107 | mathlab | BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals. | 2017 | [matlab] code is a | |
| 27605105 | java | ReliableGenome: annotation of genomic regions with high/low variant calling concordance. | 2017 | mented in [java], source c | |
| 27605102 | java | PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. | 2017 | dependent [java] tool that | |
| 27605100 | python | MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. | 2017 | mented in [python], perl and | |
| 27605100 | perl | MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. | 2017 | n python, [perl] and javas | |
| 27605100 | javascript | MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. | 2017 | perl and [javascript] and is fr | |
| 27605099 | java | OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts. | 2017 | run on a [java] ee applic | |
| 27605098 | r | DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. | 2017 | ed in the [R language] and are a | |
| 27597310 | r | NEAT: an efficient network enrichment analysis test. | 2016 | ed in the [R package] neat, whi | |
| 27592708 | r | Gene- and pathway-based association tests for multiple traits with GWAS summary statistics. | 2017 | mented in [R package] aspu, fre | |
| 27591081 | r | Precrec: fast and accurate precision-recall and ROC curve calculations in R. | 2017 | able from [CRAN] (https:// | |
| 27587701 | python | Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach. | 2016 | [python] scripts f | |
| 27587695 | r | Large-scale inference of conjunctive Bayesian networks. | 2016 | ted as an [R package] available | |
| 27587694 | mathlab | L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. | 2016 | a [matlab] implement | |
| 27587693 | python | A probabilistic model for detecting rigid domains in protein structures. | 2016 | the [python] source co | |
| 27587690 | python | Patterns of amino acid conservation in human and animal immunodeficiency viruses. | 2016 | a [python] package i | |
| 27587680 | r | A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions. | 2016 | a [R package] ummdr a | |
| 27587666 | java | PanTools: representation, storage and exploration of pan-genomic data. | 2016 | the [java] implement | |
| 27587664 | java | The Network Library: a framework to rapidly integrate network biology resources. | 2016 | eloped in [java] and avail | |
| 27587659 | python | Combining dependent P-values with an empirical adaptation of Brown's method. | 2016 | ilable in [python], r, and m | |
| 27587659 | r | Combining dependent P-values with an empirical adaptation of Brown's method. | 2016 | able as a [Bioconductor] package f | |
| 27587659 | mathlab | Combining dependent P-values with an empirical adaptation of Brown's method. | 2016 | n, r, and [matlab] and can b | |
| 27587657 | r | TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types. | 2016 | ble as an [R package] on cran ( | |
| 27585881 | r | Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets. | 2016 | lly as an [R package] ( https:/ | |
| 27585881 | mathlab | Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets. | 2016 | compiled [matlab] package ( | |
| 27578804 | python | FATSLiM: a fast and robust software to analyze MD simulations of membranes. | 2017 | ritten in [python]. source c | |
| 27565584 | java | A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data. | 2017 | a [java] standalon | |
| 27559155 | mathlab | Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. | 2016 | code for [matlab] including | |
| 27559153 | c | Discoal: flexible coalescent simulations with selection. | 2016 | ed in the [C programming] language. | |
| 27553625 | mathlab | Stepwise iterative maximum likelihood clustering approach. | 2016 | ethods. a [matlab] package o | |
| 27553489 | r | Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. | 2016 | od in the [R package] quaternar | |
| 27543791 | r | Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants. | 2017 | ended the [R package] 'robustba | |
| 27542772 | r | STAMS: STRING-assisted module search for genome wide association studies and application to autism. | 2016 | ted as an [R package] and is fr | |
| 27542771 | python | MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data. | 2016 | mented in [python] 2.7 and i | |
| 27542770 | r | DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments. | 2016 | esubs: an [R package] for flexi | |
| 27534850 | r | A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. | 2016 | plemented [R package] is availa | |
| 27522082 | r | oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. | 2016 | mented in [Bioconductor] package e | |
| 27522081 | javascript | Gene Slider: sequence logo interactive data-visualization for education and research. | 2016 | mented in [javascript] and proce | |
| 27516195 | python | BAMQL: a query language for extracting reads from BAM files. | 2016 | pysam for [python]. both all | |
| 27516195 | perl | BAMQL: a query language for extracting reads from BAM files. | 2016 | tools for [perl] and pysam | |
| 27515739 | python | LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. | 2016 | and-alone [python] library c | |
| 27515738 | r | NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. | 2016 | the [R package] is freely | |
| 27503227 | perl | SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads. | 2016 | mented in [perl] and is pu | |
| 27503226 | r | shinyGEO: a web-based application for analyzing gene expression omnibus datasets. | 2016 | ta export [and R] code gene | |
| 27503224 | python | PathScore: a web tool for identifying altered pathways in cancer data. | 2016 | mented in [python] and mysql | |
| 27503223 | r | Bayesian network feature finder (BANFF): an R package for gene network feature selection. | 2016 | anff): an [R package] for gene | |
| 27497442 | r | A novel copy number variants kernel association test with application to autism spectrum disorders studies. | 2016 | a [R package] to implem | |
| 27497440 | r | scphaser: haplotype inference using single-cell RNA-seq data. | 2016 | haser, an [R package] that phas | |
| 27497439 | python | genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools. | 2016 | en source [python] software | |
| 27493193 | perl | FARAO: the flexible all-round annotation organizer. | 2016 | mented in [perl] and is su | |
| 27480116 | r | Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment. | 2016 | ts. it is [written in R] code and | |
| 27473172 | r | RevEcoR: an R package for the reverse ecology analysis of microbiomes. | 2016 | vecor: an [R package] for the r | |
| 27466625 | mathlab | Joint sparse canonical correlation analysis for detecting differential imaging genetics modules. | 2016 | the [matlab] code is a | |
| 27465477 | r | flowVS: channel-specific variance stabilization in flow cytometry. | 2016 | ilable in [Bioconductor]. | |
| 27454116 | mathlab | A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. | 2016 | tworks in [matlab] with the | |
| 27436563 | r | Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. | 2016 | ted in an [R package] vashr ava | |
| 27412096 | javascript | MSAViewer: interactive JavaScript visualization of multiple sequence alignments. | 2016 | teractive [javascript] visualiza | |
| 27370569 | r | MethPed: an R package for the identification of pediatric brain tumor subtypes. | 2016 | thped: an [R package] for the i | |
| 27363390 | perl | A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. | 2016 | ped using [perl], bioperl | |
| 27357171 | r | Estimating and testing high-dimensional mediation effects in epigenetic studies. | 2016 | [R package], source c | |
| 27357170 | r | Network-based pathway enrichment analysis with incomplete network information. | 2016 | ilable on [CRAN]. | |
| 27354701 | python | CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. | 2016 | ritten in [python], builds o | |
| 27354695 | r | ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. | 2016 | hment: an [R package] to test f | |
| 27342648 | mathlab | TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. | 2016 | tines for [matlab] are freel | |
| 27342194 | java | EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics. | 2016 | ritten in [java] to query | |
| 27342194 | r | EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics. | 2016 | rior-fit, [written in R] to parame | |
| 27341818 | r | Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. | 2016 | ithin the [R package] jaguar, w | |
| 27334476 | r | SERAPHIM: studying environmental rasters and phylogenetically informed movements. | 2016 | ox.ac.uk/ [R package], source c | |
| 27334471 | perl | CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. | 2016 | mented in [perl], mysql an | |
| 27334001 | r | multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions. | 2016 | thods. an [R package] implement | |
| 27333889 | r | Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. | 2016 | rovide an [R package] for explo | |
| 27324198 | python | RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data. | 2016 | mented in [python] (v2.7) an | |
| 27324197 | r | Integrated gene set analysis for microRNA studies. | 2016 | ed in the [Bioconductor] library m | |
| 27323392 | r | compendiumdb: an R package for retrieval and storage of functional genomics data. | 2016 | iumdb: an [R package] for retri | |
| 27323392 | perl | compendiumdb: an R package for retrieval and storage of functional genomics data. | 2016 | mysql and [perl]. source c | |
| 27318208 | python | Statistical modeling of isoform splicing dynamics from RNA-seq time series data. | 2016 | [python] code is f | |
| 27318205 | r | NegGOA: negative GO annotations selection using ontology structure. | 2016 | he matlab [and R] codes are | |
| 27318205 | mathlab | NegGOA: negative GO annotations selection using ontology structure. | 2016 | the [matlab] and r cod | |
| 27318203 | perl | The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants. | 2016 | mented in [perl] and c and | |
| 27318199 | python | TADtool: visual parameter identification for TAD-calling algorithms. | 2016 | n or as a [python] package f | |
| 27318198 | r | Pseudotime estimation: deconfounding single cell time series. | 2016 | ilable on [CRAN] in the de | |
| 27316337 | r | PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. | 2016 | e with an [R package], assigned | |
| 27312412 | perl | RADIS: analysis of RAD-seq data for interspecific phylogeny. | 2016 | oduce the [perl] pipeline | |
| 27312411 | python | MultiQC: summarize analysis results for multiple tools and samples in a single report. | 2016 | thub, the [python] package i | |
| 27312410 | java | ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process. | 2016 | ritten in [java], open sou | |
| 27307645 | java | BioASF: a framework for automatically generating executable pathway models specified in BioPAX. | 2016 | mented in [java], is open | |
| 27307638 | c | RNAiFold2T: Constraint Programming design of thermo-IRES switches. | 2016 | ftware is [written in C] ++ and us | |
| 27307630 | r | Linear effects models of signaling pathways from combinatorial perturbation data. | 2016 | able as a [R package] at http:/ | |
| 27307614 | c | deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding. | 2016 | mented in [C language], the sour | |
| 27307611 | mathlab | Analysis of differential splicing suggests different modes of short-term splicing regulation. | 2016 | r and [matlab] codes imp | |
| 27307610 | r | A cross-species bi-clustering approach to identifying conserved co-regulated genes. | 2016 | the [R package] containin | |
| 27307609 | python | Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. | 2016 | mented in [python] and avail | |
| 27296983 | mathlab | A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits. | 2016 | mented in [matlab]. | |
| 27296982 | r | GSA-Lightning: ultra-fast permutation-based gene set analysis. | 2016 | lightning [R package] is availa | |
| 27296981 | r | CONDOP: an R package for CONdition-Dependent Operon Predictions. | 2016 | ondop: an [R package] for condi | |
| 27296979 | java | Web-based network analysis and visualization using CellMaps. | 2016 | in c and [java]. | |
| 27296979 | javascript | Web-based network analysis and visualization using CellMaps. | 2016 | available [javascript] api. | |
| 27295045 | r | Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. | 2016 | ted as an [R package], currentl | |
| 27288501 | r | RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data. | 2016 | tps://www.[Bioconductor].org/packa | |
| 27288499 | r | GenVisR: Genomic Visualizations in R. | 2016 | isr is an [R package] available | |
| 27288495 | r | Inferring the perturbation time from biological time course data. | 2016 | ion: : an [R package], detime, | |
| 27288494 | r | bdvis: visualizing biodiversity data in R. | 2016 | scribe an [R package], bdvis, w | |
| 27288492 | r | Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control. | 2016 | and as an [R package]. the c so | |
| 27283952 | java | TaggerOne: joint named entity recognition and normalization with semi-Markov Models. | 2016 | gerone, a [java] implement | |
| 27283951 | r | GHap: an R package for genome-wide haplotyping. | 2016 | ghap: an [R package] for genom | |
| 27283948 | python | pong: fast analysis and visualization of latent clusters in population genetic data. | 2016 | using the [python] package m | |
| 27273669 | r | R.JIVE for exploration of multi-source molecular data. | 2016 | intuitive [R package] to perfor | |
| 27266441 | r | HDTD: analyzing multi-tissue gene expression data. | 2016 | the [R package] hdtd is p | |
| 27259541 | java | MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. | 2016 | ritten in [java] and is pl | |
| 27256314 | r | RANKS: a flexible tool for node label ranking and classification in biological networks. | 2016 | ackage is [written in R], except f | |
| 27230384 | javascript | Crowdsourcing the nodulation gene network discovery environment. | 2016 | nd vis.js [javascript] libraries | |
| 27207944 | r | Differential rhythmicity: detecting altered rhythmicity in biological data. | 2016 | ilable on [CRAN]. | |
| 27207943 | r | Complex heatmaps reveal patterns and correlations in multidimensional genomic data. | 2016 | from the [Bioconductor] project: | |
| 27187204 | r | seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. | 2016 | mented in [R package] seqlm tha | |
| 27153821 | perl | DensityMap: a genome viewer for illustrating the densities of features. | 2016 | ghtweight [perl] program t | |
| 27153725 | python | NMRPro: an integrated web component for interactive processing and visualization of NMR spectra. | 2016 | parts: a [python] package t | |
| 27153719 | r | MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. | 2016 | an [R package] metaktsp | |
| 27153717 | python | FRED 2: an immunoinformatics framework for Python. | 2016 | ework for [python]. | |
| 27153716 | java | Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. | 2016 | in perl, [java] and javas | |
| 27153716 | perl | Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. | 2016 | mented in [perl], java and | |
| 27153716 | javascript | Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. | 2016 | java and [javascript] and jmol | |
| 27153715 | r | cit: hypothesis testing software for mediation analysis in genomic applications. | 2016 | en-source [R package] is freely | |
| 27153711 | mathlab | Simulated single molecule microscopy with SMeagol. | 2016 | l runs on [matlab] r2014 and | |
| 27153705 | mathlab | KiT: a MATLAB package for kinetochore tracking. | 2016 | kit: a [matlab] package f | |
| 27153704 | r | A web application for sample size and power calculation in case-control microbiome studies. | 2016 | erface is [written in R] code usin | |
| 27153702 | c | SweepFinder2: increased sensitivity, robustness and flexibility. | 2016 | e that is [written in C] and can b | |
| 27153696 | mathlab | ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. | 2016 | code for [matlab] and octav | |
| 27153692 | java | Reaction Decoder Tool (RDT): extracting features from chemical reactions. | 2016 | mented in [java], supporte | |
| 27153684 | r | solarius: an R interface to SOLAR for variance component analysis in pedigrees. | 2016 | ilable on [CRAN] and on gi | |
| 27153679 | r | Coala: an R framework for coalescent simulation. | 2016 | coala, an [R package] for calli | |
| 27153677 | r | Assessing statistical significance in multivariable genome wide association analysis. | 2016 | en-source [Bioconductor] package h | |
| 27153673 | python | Goldilocks: a tool for identifying genomic regions that are 'just right'. | 2016 | ilocks: a [python] package p | |
| 27153672 | r | RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. | 2016 | into the [R package] enmix, wh | |
| 27153665 | python | DOGMA: domain-based transcriptome and proteome quality assessment. | 2016 | mented in [python] and publi | |
| 27153664 | mathlab | Combenefit: an interactive platform for the analysis and visualization of drug combinations. | 2016 | ided as a [matlab] package b | |
| 27153663 | python | MEANS: python package for Moment Expansion Approximation, iNference and Simulation. | 2016 | means: [python] package f | |
| 27153661 | r | densityCut: an efficient and versatile topological approach for automatic clustering of biological data. | 2016 | ensitycut [R package] is availa | |
| 27153657 | mathlab | Spectral identification of topological domains. | 2016 | the [matlab] source co | |
| 27153654 | python | rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. | 2016 | mented in [python] and is fr | |
| 27153652 | java | ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. | 2016 | a [java] cross-pla | |
| 27153646 | javascript | TnT: a set of libraries for visualizing trees and track-based annotations for the web. | 2016 | ritten in [javascript], licensed | |
| 27153645 | r | Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data. | 2016 | ble as an [R package] at http:/ | |
| 27153642 | r | Pasha: a versatile R package for piling chromatin HTS data. | 2016 | versatile [R package] for pilin | |
| 27153639 | r | gkmSVM: an R package for gapped-kmer SVM. | 2016 | kmsvm: an [R package] for gappe | |
| 27153638 | r | Beta-Poisson model for single-cell RNA-seq data analyses. | 2016 | an [R package] bpsc for | |
| 27153635 | r | TreeQTL: hierarchical error control for eQTL findings. | 2016 | the [R package] treeqtl i | |
| 27153632 | c | hotspot: software to support sperm-typing for investigating recombination hotspots. | 2016 | otspot is [written in C]. sources | |
| 27153628 | r | flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. | 2016 | resent an [R package], flowai, | |
| 27153627 | mathlab | MEMO: multi-experiment mixture model analysis of censored data. | 2016 | mented in [matlab] and freel | |
| 27153626 | python | Tools4miRs - one place to gather all the tools for miRNA analysis. | 2016 | mented in [python] using dja | |
| 27153620 | python | MOCAT2: a metagenomic assembly, annotation and profiling framework. | 2016 | erl 5 and [python] 2.7, desi | |
| 27153620 | perl | MOCAT2: a metagenomic assembly, annotation and profiling framework. | 2016 | mented in [perl] 5 and pyt | |
| 27153619 | python | ProtPOS: a python package for the prediction of protein preferred orientation on a surface. | 2016 | rotpos: a [python] package f | |
| 27153616 | python | SBtab: a flexible table format for data exchange in systems biology. | 2016 | and-alone [python] code cont | |
| 27153616 | r | SBtab: a flexible table format for data exchange in systems biology. | 2016 | l, matlab [and R]. the stan | |
| 27153616 | mathlab | SBtab: a flexible table format for data exchange in systems biology. | 2016 | ms excel, [matlab] and r. th | |
| 27153605 | javascript | pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data. | 2016 | eup.js: a [javascript] library f | |
| 27153599 | r | HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. | 2016 | from the [Bioconductor] project: | |
| 27153598 | r | FREGAT: an R package for region-based association analysis. | 2016 | regat: an [R package] for regio | |
| 27153596 | r | OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA. | 2016 | ybs is an [R package] available | |
| 27153595 | python | MGEScan: a Galaxy-based system for identifying retrotransposons in genomes. | 2016 | h mpi and [python] threading | |
| 27153592 | r | Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. | 2016 | ted as an [R package] available | |
| 27153588 | java | Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project. | 2016 | -friendly [java] tool to e | |
| 27153587 | python | jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data. | 2016 | tandalone [python] applicati | |
| 27153585 | r | EBglmnet: a comprehensive R package for sparse generalized linear regression models. | 2016 | rehensive [R package] for spars | |
| 27153580 | r | chromPlot: visualization of genomic data in chromosomal context. | 2016 | ttp://www.[Bioconductor].org | |
| 27153579 | perl | ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. | 2016 | [perl] script fo | |
| 27153577 | mathlab | Analysis of CFSE time-series data using division-, age- and label-structured population models. | 2016 | the [matlab] source co | |
| 27153575 | python | mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. | 2016 | c ++ and [python], and supp | |
| 27153574 | r | SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. | 2016 | conductor [R package] to invest | |
| 27153572 | javascript | Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization. | 2016 | html and [javascript] code. voe | |
| 27146037 | r | readat: An R package for reading and working with SomaLogic ADAT files. | 2016 | eadat: an [R package] for readi | |
| 27143038 | javascript | QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. | 2016 | advanced [javascript] framework | |
| 27117841 | mathlab | eSTGt: a programming and simulation environment for population dynamics. | 2016 | or using [matlab]'s command | |
| 27113060 | r | Erratum to: 'CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments'. | 2016 | ompgo: an [R package] for compa | |
| 27094401 | r | Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves. | 2016 | urver: an [R package] for obtai | |
| 27083325 | python | UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. | 2016 | mented in [python] and runs | |
| 27071656 | python | Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations. | 2016 | a set of [python] modules u | |
| 27059780 | java | CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies. | 2016 | ncy using [java] or c++. i | |
| 27059780 | c++ | CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies. | 2016 | g java or [C++]. intermed | |
| 27059780 | r | CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies. | 2016 | on in the [R package] collapsab | |
| 27044654 | java | The systems biology format converter. | 2016 | ritten in [java] and can b | |
| 27044654 | mathlab | The systems biology format converter. | 2016 | sbgn-ml, [matlab], octave, | |
| 27029470 | r | Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments. | 2016 | rovide an [R package] ssizerna | |
| 27005934 | r | caOmicsV: an R package for visualizing multidimensional cancer genomic data. | 2016 | micsv: an [R package] for visua | |
| 27001666 | r | Leveraging protein quaternary structure to identify oncogenic driver mutations. | 2016 | eins. the [R package] is availa | |
| 26968614 | r | GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. | 2016 | standard [Bioconductor] extension | |
| 26964749 | mathlab | PeTTSy: a computational tool for perturbation analysis of complex systems biology models. | 2016 | ckage for [matlab] which imp | |
| 26961892 | r | FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data. | 2016 | efficient [R package] that fill | |
| 26961516 | perl | Geena 2, improved automated analysis of MALDI/TOF mass spectra. | 2016 | n php and [perl]. input an | |
| 26956433 | r | Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). | 2016 | (2)>0.90 [and R] m s e<4.0 | |
| 26951498 | r | Testing for association between RNA-Seq and high-dimensional data. | 2016 | sion. the [R package] globalseq | |
| 26873932 | java | An empirical Bayes change-point model for identifying 3' and 5' alternative splicing by next-generation RNA sequencing. | 2016 | mented in [java] and can b | |
| 26861823 | python | Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. | 2016 | ted using [python] 2.7 and c | |
| 26861822 | r | Measuring the spatial correlations of protein binding sites. | 2016 | an [R package] is availa | |
| 26861821 | r | TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. | 2016 | ronco: an [R package] for the i | |
| 26861819 | mathlab | MOCCASIN: converting MATLAB ODE models to SBML. | 2016 | onverting [matlab] ode model | |
| 26860319 | r | LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. | 2016 | aca is an [R package] available | |
| 26860128 | r | Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. | 2016 | a the sim [Bioconductor] package. | |
| 26833345 | r | GiANT: gene set uncertainty in enrichment analysis. | 2016 | ilable on [CRAN]. | |
| 26833343 | mathlab | Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems. | 2016 | able as a [matlab] script in | |
| 26833341 | mathlab | Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. | 2016 | a [matlab] package o | |
| 26830926 | python | ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research. | 2016 | ritten in [python] with mult | |
| 26819473 | javascript | BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. | 2016 | ve circos [javascript] library f | |
| 26819470 | r | Differential methylation analysis for BS-seq data under general experimental design. | 2016 | ilable as [Bioconductor] package d | |
| 26819469 | python | FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector. | 2016 | ritten in [python] and runs | |
| 26819101 | javascript | DNAism: exploring genomic datasets on the web with Horizon Charts. | 2016 | existing [javascript] library ( | |
| 26818685 | r | A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. | 2016 | lysis. an [R package] named as | |
| 26803162 | r | DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures. | 2016 | able from [Bioconductor]. | |
| 26803161 | r | PAA: an R/bioconductor package for biomarker discovery with protein microarrays. | 2016 | ttp://www.[Bioconductor].org/packa | |
| 26803158 | r | FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees. | 2016 | amagg: an [R package] to evalua | |
| 26803157 | r | lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection. | 2016 | sy-to-use [R package] that prov | |
| 26801960 | mathlab | Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method. | 2016 | the [matlab] code and | |
| 26794317 | perl | The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. | 2016 | xtensible [perl] library w | |
| 26794315 | r | TFBSTools: an R/bioconductor package for transcription factor binding site analysis. | 2016 | from the [Bioconductor] website ( | |
| 26791995 | r | Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. | 2016 | [Bioconductor]'s enrichm | |
| 26787665 | r | Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. | 2016 | .html the [R package] rsampletr | |
| 26773132 | perl | SIRAH tools: mapping, backmapping and visualization of coarse-grained models. | 2016 | ritten in [perl], tcl, or | |
| 26772743 | c++ | A computational method for genotype calling in family-based sequencing data. | 2016 | ntly in a [C++] program f | |
| 26769317 | python | Realizing privacy preserving genome-wide association studies. | 2016 | a [python] implement | |
| 26757899 | python | Aligning the unalignable: bacteriophage whole genome alignments. | 2016 | trains. a [python] implement | |
| 26755624 | python | Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. | 2016 | mented in [python] and is fr | |
| 26753519 | r | Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. | 2016 | es in the [R package] bapred av | |
| 26743507 | r | OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. | 2016 | ble as an [R package] along wit | |
| 26733452 | r | Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. | 2016 | h2ppi: an [R package] to predic | |
| 26729218 | java | Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. | 2016 | en-source [java] library a | |
| 26708336 | r | rCGH: a comprehensive array-based genomic profile platform for precision medicine. | 2016 | the rcgh [R package] is availa | |
| 26708334 | javascript | HitWalker2: visual analytics for precision medicine and beyond. | 2016 | neo4j and [javascript] (d3.js an | |
| 26685309 | mathlab | Fast integration-based prediction bands for ordinary differential equation models. | 2016 | based on [matlab] and freel | |
| 26685307 | r | traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. | 2016 | raser: an [R package] for perfo | |
| 26685306 | r | PaxtoolsR: pathway analysis in R using Pathway Commons. | 2016 | conductor [R package] repositor | |
| 26685305 | mathlab | FluxModeCalculator: an efficient tool for large-scale flux mode computation. | 2016 | ration in [matlab], called f | |
| 26677932 | python | PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. | 2015 | n php and [python] programmi | |
| 26668005 | r | DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. | 2016 | ogramming [language r] and is fr | |
| 26656933 | c | BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. | 2016 | biofvm is [written in C] ++ with p | |
| 26656932 | python | Sequence database versioning for command line and Galaxy bioinformatics servers. | 2016 | ritten in [python] and relea | |
| 26656570 | r | Adaptive gene- and pathway-trait association testing with GWAS summary statistics. | 2016 | mented in [R package] aspu, fre | |
| 26656004 | r | PharmacoGx: an R package for analysis of large pharmacogenomic datasets. | 2016 | acogx: an [R package] for analy | |
| 26652794 | java | MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development. | 2015 | dependent [java] programin | |
| 26644415 | java | Joint detection of copy number variations in parent-offspring trios. | 2016 | nation of [java] and r is | |
| 26644415 | r | Joint detection of copy number variations in parent-offspring trios. | 2016 | n of java [and R] is freely | |
| 26637292 | c | Maligner: a fast ordered restriction map aligner. | 2016 | ftware is [written in C] ++ and is | |
| 26635141 | r | rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. | 2016 | cellminer [R package] provides | |
| 26628587 | mathlab | IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. | 2016 | mented in [matlab] and be do | |
| 26607490 | r | Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. | 2016 | able from [Bioconductor]. http://w | |
| 26589280 | c++ | hybridSPAdes: an algorithm for hybrid assembly of short and long reads. | 2016 | mented in [C++] as a part | |
| 26589278 | r | Reliable ABC model choice via random forests. | 2016 | ed in the [R package] abcrf ava | |
| 26589277 | python | SomVarIUS: somatic variant identification from unpaired tissue samples. | 2016 | ritten in [python] 2.7 and a | |
| 26589276 | perl | ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. | 2016 | -threaded [perl] software | |
| 26589275 | python | FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting. | 2016 | ritten in [python] and is av | |
| 26589274 | r | LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations. | 2016 | plorer is [written in R] using the | |
| 26589273 | mathlab | CellTracker (not only) for dummies. | 2016 | ritten in [matlab] (the math | |
| 26577052 | r | DiffLogo: a comparative visualization of sequence motifs. | 2015 | -friendly [R package] for visua | |
| 26568633 | python | Optimal design of gene knockout experiments for gene regulatory network inference. | 2016 | atlab and [python] scripts o | |
| 26568633 | mathlab | Optimal design of gene knockout experiments for gene regulatory network inference. | 2016 | [matlab] and pytho | |
| 26568624 | c++ | Optimal seed solver: optimizing seed selection in read mapping. | 2016 | solver in [C++] at: https | |
| 26558877 | c | Two molecular measures of relatedness based on haplotype sharing. | 2015 | founders. [using C] in linear | |
| 26556386 | r | contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples. | 2016 | an [R package] contamde | |
| 26556385 | r | Specific identification and quantification of circular RNAs from sequencing data. | 2016 | ns by our [R package] circtest | |
| 26556383 | java | Realtime analysis and visualization of MinION sequencing data with npReader. | 2016 | ritten in [java] and is fr | |
| 26553913 | r | CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array. | 2016 | ted as an [R package]. the pack | |
| 26552737 | java | From raw data to data-analysis for magnetic resonance spectroscopy--the missing link: jMRUI2XML. | 2015 | 2xml is a [java] solution | |
| 26545824 | python | Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. | 2016 | mented in [python] and suppo | |
| 26545822 | r | Comparison of genetic variants in matched samples using thesaurus annotation. | 2016 | ted in an [R package] available | |
| 26545820 | r | Probabilistic models of genetic variation in structured populations applied to global human studies. | 2016 | conductor [R package] called lf | |
| 26543176 | mathlab | Shape component analysis: structure-preserving dimension reduction on biological shape spaces. | 2016 | s made in [matlab] and suppo | |
| 26543171 | r | TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates. | 2016 | tess: an [R package] for effic | |
| 26538306 | python | Fizzy: feature subset selection for metagenomics. | 2015 | ped a new [python] command l | |
| 26537733 | c++ | BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms. | 2015 | ovided in [C++] for infor | |
| 26537417 | python | ODTbrain: a Python library for full-view, dense diffraction tomography. | 2015 | tbrain: a [python] library f | |
| 26530724 | python | PHYLUCE is a software package for the analysis of conserved genomic loci. | 2016 | itten for [python] 2.7. phyl | |
| 26520854 | java | Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks. | 2016 | m made in [java] and the f | |
| 26519502 | r | Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. | 2016 | mented in [R package] ipbt, whi | |
| 26515826 | javascript | Protael: protein data visualization library for the web. | 2016 | tael is a [javascript] library f | |
| 26515824 | c++ | SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. | 2016 | nted with [C++] and is av | |
| 26515822 | perl | PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes. | 2016 | pdates in [perl] and it is | |
| 26515818 | r | EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes. | 2016 | the [R package] is availa | |
| 26514335 | r | ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. | 2015 | paseq: an [R package] for topol | |
| 26508760 | r | RVFam: an R package for rare variant association analysis with family data. | 2016 | rvfam: an [R package] for rare | |
| 26508757 | r | LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. | 2016 | [R package] available | |
| 26508755 | r | caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. | 2016 | pools: an [R package] for explo | |
| 26504142 | python | Pycellerator: an arrow-based reaction-like modelling language for biological simulations. | 2016 | erator, a [python] library f | |
| 26504139 | java | IsoMIF Finder: online detection of binding site molecular interaction field similarities. | 2016 | jsmol (no [java] plugin re | |
| 26500152 | r | funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types. | 2016 | onorm: an [R package] for norma | |
| 26493835 | javascript | PDB-Explorer: a web-based interactive map of the protein data bank in shape space. | 2015 | mented in [javascript] in a plat | |
| 26487736 | perl | RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data. | 2016 | ritten in [perl] and is fr | |
| 26476781 | python | A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. | 2016 | nux using [python] under fre | |
| 26476780 | java | Scalable clustering algorithms for continuous environmental flow cytometry. | 2016 | mented in [java] for use w | |
| 26471456 | python | Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. | 2016 | mented in [python] with flas | |
| 26468003 | r | BiTrinA--multiscale binarization and trinarization with quality analysis. | 2016 | ilable on [CRAN]. | |
| 26458889 | c++ | A multi-objective optimization approach accurately resolves protein domain architectures. | 2016 | mented in [C++] and the s | |
| 26454281 | python | CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads. | 2016 | cssscl: a [python] package t | |
| 26454280 | python | SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. | 2016 | mented in [python], and its | |
| 26454279 | c++ | Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. | 2016 | mented in [C++]. the sour | |
| 26454276 | java | Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. | 2016 | mented in [java] along wit | |
| 26454275 | python | miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis. | 2016 | mented in [python] (version | |
| 26454273 | python | Jflow: a workflow management system for web applications. | 2016 | ion and a [python] library p | |
| 26454094 | python | Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. | 2016 | opment of [python] and web-s | |
| 26449931 | r | CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. | 2016 | n via the [R package] 'cpgfilte | |
| 26449930 | python | HapFlow: visualizing haplotypes in sequencing data. | 2016 | flow is a [python] applicati | |
| 26446136 | javascript | The new protein topology graph library web server. | 2016 | d in php, [javascript], postgres | |
| 26446133 | mathlab | SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. | 2016 | oolbox: a [matlab] toolbox f | |
| 26446060 | r | Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls. | 2016 | ed in the [R package] cherry. | |
| 26445311 | r | DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. | 2015 | decipher [R package] and sourc | |
| 26428291 | c++ | ALP & FALP: C++ libraries for pairwise local alignment E-values. | 2016 | p & falp: [C++] libraries | |
| 26428289 | r | Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology. | 2016 | ilable on [Bioconductor] http://ww | |
| 26428288 | c++ | Pseudoknots in RNA folding landscapes. | 2016 | mented in [C++] as standa | |
| 26424859 | r | Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis. | 2016 | en source [R package] available | |
| 26424858 | r | regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. | 2016 | ner is an [R package] that impl | |
| 26424855 | r | missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform. | 2016 | ethyl: an [R package] for analy | |
| 26423836 | javascript | Density-based parallel skin lesion border detection with webCL. | 2015 | ebcl is a [javascript] binding o | |
| 26423515 | mathlab | Efficient experimental design for uncertainty reduction in gene regulatory networks. | 2015 | cantly. a [matlab] software | |
| 26415849 | r | NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference. | 2015 | chmark: a [Bioconductor] package f | |
| 26415725 | c++ | XPIWIT--an XML pipeline wrapper for the Insight Toolkit. | 2016 | ard-coded [C++] pipelines | |
| 26415723 | r | ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. | 2016 | [R package] and sourc | |
| 26415722 | javascript | Cytoscape.js: a graph theory library for visualisation and analysis. | 2016 | mented in [javascript]. document | |
| 26411870 | c++ | JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. | 2016 | mented in [C++], supporte | |
| 26411869 | c++ | CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data. | 2016 | the [C++] and qt so | |
| 26411867 | r | XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. | 2016 | xlmap: an [R package] to visual | |
| 26399714 | python | htsint: a Python library for sequencing pipelines that combines data through gene set generation. | 2015 | htsint: a [python] library f | |
| 26384762 | c++ | Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles. | 2015 | top of a [C++] implement | |
| 26384762 | javascript | Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles. | 2015 | marily in [javascript], on top o | |
| 26382197 | java | NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. | 2016 | mented in [java] with supp | |
| 26382193 | perl | ICT: isotope correction toolbox. | 2016 | language [perl] and, ther | |
| 26374744 | r | mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics. | 2015 | ed in the [R package], which is | |
| 26374641 | r | A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures. | 2015 | ed in the [R package] coxboost | |
| 26369703 | python | PyPDB: a Python API for the Protein Data Bank. | 2016 | pypdb: a [python] api for t | |
| 26363176 | c++ | markophylo: Markov chain analysis on phylogenetic trees. | 2016 | ritten in [C++] and the i | |
| 26363176 | r | markophylo: Markov chain analysis on phylogenetic trees. | 2016 | and fast [R package] is introd | |
| 26363029 | java | An algorithm for automated layout of process description maps drawn in SBGN. | 2016 | orithm in [java] is availa | |
| 26363028 | c++ | BamHash: a checksum program for verifying the integrity of sequence data. | 2016 | mented in [C++], gpl lice | |
| 26358728 | c++ | SeDuS: segmental duplication simulator. | 2016 | mented in [C++] and can b | |
| 26358727 | r | Group and sparse group partial least square approaches applied in genomics context. | 2016 | rehensive [R package] called sg | |
| 26342229 | r | BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. | 2016 | or matlab [and R]. | |
| 26342229 | mathlab | BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. | 2016 | lable for [matlab] and r. | |
| 26338769 | mathlab | Discovering hospital admission patterns using models learnt from electronic hospital records. | 2015 | full [matlab] source co | |
| 26338767 | r | DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. | 2015 | diggit: a [Bioconductor] package t | |
| 26329719 | r | CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. | 2015 | ompgo: an [R package] for compa | |
| 26328606 | java | Pan-Tetris: an interactive visualisation for Pan-genomes. | 2015 | tetris, a [java] based int | |
| 26328469 | r | VisRseq: R-based visual framework for analysis of sequencing data. | 2015 | s such as [Bioconductor]. to addre | |
| 26323718 | c++ | NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. | 2015 | mented in [C++] and is av | |
| 26323716 | c | BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure. | 2015 | ptools--a [C programming] library a | |
| 26323713 | c++ | RASER: reads aligner for SNPs and editing sites of RNA. | 2015 | ritten in [C++] and freel | |
| 26319390 | c++ | Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. | 2016 | mented in [C++] and has b | |
| 26319221 | c++ | BS-SNPer: SNP calling in bisulfite-seq data. | 2015 | ritten in [C++] and perl, | |
| 26319221 | perl | BS-SNPer: SNP calling in bisulfite-seq data. | 2015 | n c++ and [perl], and is f | |
| 26315911 | r | msa: an R package for multiple sequence alignment. | 2015 | msa: an [R package] for multi | |
| 26315910 | python | Identification of hierarchical chromatin domains. | 2016 | a [python] implement | |
| 26315909 | c++ | glmgraph: an R package for variable selection and predictive modeling of structured genomic data. | 2015 | in r and [C++] armadillo | |
| 26315909 | r | glmgraph: an R package for variable selection and predictive modeling of structured genomic data. | 2015 | graph: an [R package] for varia | |
| 26315908 | c | HiXCorr: a portable high-speed XCorr engine for high-resolution tandem mass spectrometry. | 2015 | eloped in [C language]. hence, o | |
| 26315907 | c++ | Fast and accurate approximate inference of transcript expression from RNA-seq data. | 2015 | in r and [C++], and are | |
| 26315907 | r | Fast and accurate approximate inference of transcript expression from RNA-seq data. | 2015 | he bitseq [Bioconductor] package. | |
| 26315904 | java | LIBRA: LIgand Binding site Recognition Application. | 2015 | eloped in [java] se 7 with | |
| 26315903 | perl | Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences. | 2015 | mented in [perl] and freel | |
| 26298294 | python | Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. | 2015 | perl, and [python]. subseque | |
| 26298294 | perl | Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. | 2015 | s like r, [perl], and pyth | |
| 26286809 | python | svviz: a read viewer for validating structural variants. | 2015 | mented in [python] and freel | |
| 26283514 | r | diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. | 2015 | iffhic: a [Bioconductor] package t | |
| 26283310 | r | SIMAT: GC-SIM-MS data analysis tool. | 2015 | uce a new [R package] called si | |
| 26275896 | r | DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism. | 2015 | iadrm: an [R package] for estim | |
| 26272984 | r | motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. | 2015 | ed within [Bioconductor]. | |
| 26261223 | java | Vizardous: interactive analysis of microbial populations with single cell resolution. | 2015 | xecutable [java] archive a | |
| 26254488 | java | BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. | 2015 | ritten in [java]. source c | |
| 26249815 | r | cgmisc: enhanced genome-wide association analyses and visualization. | 2015 | gmisc, an [R package] that enab | |
| 26249810 | python | NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. | 2015 | mented in [python] and c/c++ | |
| 26249809 | python | ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. | 2015 | eloped in [python] and runs | |
| 26243017 | r | NAM: association studies in multiple populations. | 2015 | e nam, an [R package] that allo | |
| 26231430 | r | stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation. | 2015 | ssnet, an [R package] that inte | |
| 26231427 | python | An efficient algorithm for the extraction of HGVS variant descriptions from sequences. | 2015 | code and [python] interface | |
| 26231427 | c++ | An efficient algorithm for the extraction of HGVS variant descriptions from sequences. | 2015 | .nl). the [C++] source co | |
| 26231426 | r | MICC: an R package for identifying chromatin interactions from ChIA-PET data. | 2015 | micc: an [R package] for ident | |
| 26227145 | python | BackCLIP: a tool to identify common background presence in PAR-CLIP datasets. | 2015 | mented in [python]. the comm | |
| 26227143 | perl | SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. | 2015 | 1.2 is a [perl] program w | |
| 26220962 | r | MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics. | 2015 | the [R package] mettailor | |
| 26220961 | r | Designing alternative splicing RNA-seq studies. Beyond generic guidelines. | 2015 | ge at www.[Bioconductor].org/packa | |
| 26209431 | r | dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. | 2015 | xtend: an [R package] for visua | |
| 26208945 | python | Object-based representation and analysis of light and electron microscopic volume data using Blender. | 2015 | embedded [python] applicati | |
| 26206305 | python | Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. | 2015 | aded as a [python] function | |
| 26206305 | mathlab | Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. | 2015 | tion or a [matlab] script al | |
| 26198102 | perl | Roary: rapid large-scale prokaryote pan genome analysis. | 2015 | mented in [perl] and is fr | |
| 26187943 | r | RxnSim: a tool to compare biochemical reactions. | 2015 | network, [CRAN] (http://c | |
| 26163694 | r | SomaticSignatures: inferring mutational signatures from single-nucleotide variants. | 2015 | the [R package] somaticsi | |
| 26163509 | r | TiMEx: a waiting time model for mutually exclusive cancer alterations. | 2016 | conductor [R package] at www.bs | |
| 26160651 | python | Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. | 2015 | inimalist [python] implement | |
| 26153515 | java | LayerCake: a tool for the visual comparison of viral deep sequencing data. | 2015 | ework for [java]. | |
| 26148744 | r | DINGO: differential network analysis in genomics. | 2015 | [R package] at: odin. | |
| 26142188 | mathlab | Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. | 2015 | nment for [matlab] that pion | |
| 26142186 | c++ | al3c: high-performance software for parameter inference using Approximate Bayesian Computation. | 2015 | t al3c, a [C++] framework | |
| 26130249 | python | YBYRÁ facilitates comparison of large phylogenetic trees. | 2015 | ritten in [python], hence th | |
| 26130577 | r | A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. | 2015 | en-source [R package] at that i | |
| 26130576 | perl | Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff. | 2015 | a [perl] script fo | |
| 26130574 | python | ProFET: Feature engineering captures high-level protein functions. | 2015 | mented in [python] and adapt | |
| 26130573 | r | Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. | 2016 | ilable as [R package] 'ngs.mc' | |
| 26115986 | python | nextflu: real-time tracking of seasonal influenza virus evolution in humans. | 2015 | [python] and javas | |
| 26115986 | javascript | nextflu: real-time tracking of seasonal influenza virus evolution in humans. | 2015 | ython and [javascript] source co | |
| 26112292 | perl | damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. | 2015 | mented in [perl] and is co | |
| 26112291 | java | Real-time multi-view deconvolution. | 2015 | olution', [java] wrappers | |
| 26112290 | r | biRte: Bayesian inference of context-specific regulator activities and transcriptional networks. | 2015 | ilable on [Bioconductor] (http://b | |
| 26099265 | c++ | Bandage: interactive visualization of de novo genome assemblies. | 2015 | mented in [C++] and suppo | |
| 26099264 | r | Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. | 2015 | e sincell [R package] implement | |
| 26093150 | javascript | GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. | 2015 | ritten in [javascript] using the | |
| 26093147 | r | An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics. | 2015 | nd in the [R package] phylodyn | |
| 26092860 | r | atSNP: transcription factor binding affinity testing for regulatory SNP detection. | 2015 | efficient [R package] for ident | |
| 26088801 | r | Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map. | 2015 | e and the [R package] are freel | |
| 26085504 | mathlab | Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks. | 2015 | the [matlab] implement | |
| 26085503 | python | libRoadRunner: a high performance SBML simulation and analysis library. | 2015 | rough its [python] interface | |
| 26085503 | c++ | libRoadRunner: a high performance SBML simulation and analysis library. | 2015 | s via its [C++] and c bin | |
| 26085503 | mathlab | libRoadRunner: a high performance SBML simulation and analysis library. | 2015 | e apis of [matlab] ( wwwmath | |
| 26079347 | java | JSBML 1.0: providing a smorgasbord of options to encode systems biology models. | 2015 | cial pure [java] programmi | |
| 26076722 | mathlab | REDEMPTION: reduced dimension ensemble modeling and parameter estimation. | 2015 | through a [matlab] user inte | |
| 26072515 | mathlab | Inferring orthologous gene regulatory networks using interspecies data fusion. | 2015 | [matlab] code is a | |
| 26072513 | c++ | Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. | 2015 | [C++] and matla | |
| 26072513 | mathlab | Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. | 2015 | c++ and [matlab] code avai | |
| 26072511 | python | Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. | 2015 | able as a [python] package ( | |
| 26072509 | python | IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. | 2015 | a c++ and [python] program r | |
| 26072509 | c++ | IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. | 2015 | able as a [C++] and pytho | |
| 26072506 | mathlab | Using collective expert judgements to evaluate quality measures of mass spectrometry images. | 2015 | y and the [matlab] source co | |
| 26072499 | python | A generic methodological framework for studying single cell motility in high-throughput time-lapse data. | 2015 | [python] code and | |
| 26072472 | java | MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. | 2015 | ritten in [java] and pytho | |
| 26072472 | python | MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. | 2015 | java and [python]. it is op | |
| 26069263 | java | IBS: an illustrator for the presentation and visualization of biological sequences. | 2015 | mented in [java], while th | |
| 26069263 | javascript | IBS: an illustrator for the presentation and visualization of biological sequences. | 2015 | html5 and [javascript]. both the | |
| 26063839 | r | oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. | 2015 | conductor [R package]. | |
| 26059717 | python | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. | 2015 | mented in [python] and datas | |
| 26056047 | c++ | Clotho: addressing the scalability of forward time population genetic simulation. | 2015 | tion as a [C++] template | |
| 26055961 | c++ | Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. | 2015 | en source [C++] implement | |
| 26051821 | python | Automatising the analysis of stochastic biochemical time-series. | 2015 | dependent [python] tool to a | |
| 26051409 | java | adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies. | 2015 | ritten in [java] j2ee, as | |
| 26049161 | bash | GeIST: a pipeline for mapping integrated DNA elements. | 2015 | nation of [bash] shell scr | |
| 26049161 | perl | GeIST: a pipeline for mapping integrated DNA elements. | 2015 | pting and [perl]. geist is | |
| 26048599 | python | Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons. | 2015 | [python] code is a | |
| 26040457 | javascript | A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data. | 2015 | n php and [javascript]. | |
| 26040456 | c++ | Assembling short reads from jumping libraries with large insert sizes. | 2015 | mented in [C++] as a part | |
| 26034064 | r | FourCSeq: analysis of 4C sequencing data. | 2015 | ed in the [R package] fourcseq | |
| 26026169 | python | DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. | 2015 | disvis, a [python] package a | |
| 26026168 | r | lpNet: a linear programming approach to reconstruct signal transduction networks. | 2015 | ach as an [R package] available | |
| 26026138 | c | QVZ: lossy compression of quality values. | 2015 | qvz is [written in C] and can b | |
| 26026137 | c++ | ACE: accurate correction of errors using K-mer tries. | 2015 | mented in [C++] and runs | |
| 26026136 | r | Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis. | 2015 | ed in the [R package] binda, wh | |
| 26017500 | r | tcR: an R package for T cell receptor repertoire advanced data analysis. | 2015 | tcr: an [R package] for t cel | |
| 26017358 | r | MANTIS: an R package that simulates multilocus models of pathogen evolution. | 2015 | antis: an [R package] that simu | |
| 26007226 | python | IgSimulator: a versatile immunosequencing simulator. | 2015 | a c++ and [python] program r | |
| 26007226 | c++ | IgSimulator: a versatile immunosequencing simulator. | 2015 | able as a [C++] and pytho | |
| 26002886 | mathlab | Diffusion maps for high-dimensional single-cell analysis of differentiation data. | 2015 | the [matlab] implement | |
| 26002885 | r | Bayesian mixture analysis for metagenomic community profiling. | 2015 | friendly [R package], freely a | |
| 26002884 | r | tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation. | 2015 | en-source [R package] tmle.npvi | |
| 26002883 | r | pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. | 2015 | omics: an [R package] for pathw | |
| 25995232 | python | When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. | 2015 | [python] scripts t | |
| 25995231 | r | ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. | 2015 | (≥5.18.1) [and R] (≥3.1.1) | |
| 25995231 | perl | ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. | 2015 | ritten in [perl] and can b | |
| 25991004 | r | affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. | 2015 | fy2sv: an [R package] to pre-pr | |
| 25987568 | python | TRAL: tandem repeat annotation library. | 2015 | en-source [python] 3 library | |
| 25987567 | c++ | IMSEQ--a fast and error aware approach to immunogenetic sequence analysis. | 2015 | mented in [C++] using the | |
| 25982853 | java | ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. | 2015 | ed in the [java] programmi | |
| 25980407 | python | NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. | 2015 | en-source [python] module; b | |
| 25979472 | r | Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. | 2015 | ay offers [Bioconductor] users enh | |
| 25972088 | r | ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. | 2015 | ted as an [R package]. the isop | |
| 25971991 | r | GENLIB: an R package for the analysis of genealogical data. | 2015 | enlib: an [R package] for the a | |
| 25971742 | javascript | GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. | 2015 | ichr adds [javascript] code to g | |
| 25971741 | r | Fast parametric time warping of peak lists. | 2015 | /ptw) and [CRAN] (http://c | |
| 25971740 | r | CAPRI: efficient inference of cancer progression models from cross-sectional data. | 2015 | oncology [R package] and is fr | |
| 25968113 | python | Domain similarity based orthology detection. | 2015 | sed using [python] and c++ l | |
| 25968113 | c++ | Domain similarity based orthology detection. | 2015 | ython and [C++] languages | |
| 25964631 | r | GOplot: an R package for visually combining expression data with functional analysis. | 2015 | oplot: an [R package] for visua | |
| 25962835 | r | A multi-view genomic data simulator. | 2015 | sses. the [R package] mvbiodata | |
| 25957349 | r | Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. | 2015 | en-source [R package] and appli | |
| 25957348 | r | INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. | 2015 | ect is an [R package] for the i | |
| 25951947 | r | Performance of a blockwise approach in variable selection using linkage disequilibrium information. | 2015 | ed in the [R package] bald (blo | |
| 25948716 | r | pez: phylogenetics for the environmental sciences. | 2015 | pez is an [R package] that perm | |
| 25943746 | r | Estimation of the methylation pattern distribution from deep sequencing data. | 2015 | in the r [Bioconductor] package m | |
| 25943565 | r | Controlling false discoveries in high-dimensional situations: boosting with stability selection. | 2015 | available [R package] stabs (ht | |
| 25940563 | javascript | Phylesystem: a git-based data store for community-curated phylogenetic estimates. | 2015 | eployed a [javascript] applicati | |
| 25940562 | java | HTT-DB: horizontally transferred transposable elements database. | 2015 | based on [java] and mysql | |
| 25933606 | python | Pydna: a simulation and documentation tool for DNA assembly strategies using python. | 2015 | ies using [python]. | |
| 25931516 | c++ | 'Flatten plus': a recent implementation in WSxM for biological research. | 2015 | mented in [C++] supported | |
| 25928861 | r | Moment based gene set tests. | 2015 | available [Bioconductor] package, | |
| 25928765 | r | coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns. | 2015 | comet, an [R package] and onlin | |
| 25926345 | r | Polyester: simulating RNA-seq datasets with differential transcript expression. | 2015 | ter is an [R package] designed | |
| 25924931 | r | plethy: management of whole body plethysmography data in R. | 2015 | rt of the [Bioconductor] project h | |
| 25924884 | c++ | UrQt: an efficient software for the Unsupervised Quality trimming of NGS data. | 2015 | mented in [C++] in an eff | |
| 25913208 | r | phylogeo: an R package for geographic analysis and visualization of microbiome data. | 2015 | logeo: an [R package] for geogr | |
| 25913205 | mathlab | Genome-scale strain designs based on regulatory minimal cut sets. | 2015 | [matlab] code and | |
| 25913204 | r | chipPCR: an R package to pre-process raw data of amplification curves. | 2015 | ippcr: an [R package] to pre-pr | |
| 25910694 | java | ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. | 2015 | ritten in [java], enables | |
| 25908790 | r | MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies. | 2015 | imeta: an [R package] for meta- | |
| 25900919 | r | edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test. | 2015 | gerun: an [R package] for sensi | |
| 25888166 | r | micropan: an R-package for microbial pan-genomics. | 2015 | resent an [R package] for the s | |
| 25888118 | java | CHEXVIS: a tool for molecular channel extraction and visualization. | 2015 | th latest [java] plug-in. | |
| 25887779 | java | OTO: Ontology Term Organizer. | 2015 | built in [java]. | |
| 25887573 | c++ | Automatic segmentation of deep intracerebral electrodes in computed tomography scans. | 2015 | en source [C++] prototype | |
| 25887481 | c++ | Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants. | 2015 | eloped in [C++] and is av | |
| 25886992 | r | Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. | 2015 | e leading [R package] for qtl s | |
| 25886979 | mathlab | FastMotif: spectral sequence motif discovery. | 2015 | the [matlab] code of f | |
| 25885646 | c | FlowClus: efficiently filtering and denoising pyrosequenced amplicons. | 2015 | s); it is [written in C] and suppo | |
| 25884684 | c++ | histoneHMM: Differential analysis of histone modifications with broad genomic footprints. | 2015 | ritten in [C++] and compi | |
| 25884684 | r | histoneHMM: Differential analysis of histone modifications with broad genomic footprints. | 2015 | led as an [R package]. it runs | |
| 25861968 | python | MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. | 2015 | code in [python] is at htt | |
| 25847007 | r | EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. | 2015 | an [R package] containin | |
| 25847006 | r | Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data. | 2015 | an [R package] to run a | |
| 25838463 | python | do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations. | 2015 | ncludes a [python] module dn | |
| 25812745 | r | KeBABS: an R package for kernel-based analysis of biological sequences. | 2015 | ebabs: an [R package] for kerne | |
| 25805722 | python | Identification of cell types from single-cell transcriptomes using a novel clustering method. | 2015 | atlab and [python]. the sour | |
| 25805722 | mathlab | Identification of cell types from single-cell transcriptomes using a novel clustering method. | 2015 | mented in [matlab] and pytho | |
| 25792553 | r | A robust approach for identifying differentially abundant features in metagenomic samples. | 2015 | an [R package] for raida | |
| 25788625 | python | Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. | 2015 | efficient [python] visualiza | |
| 25788622 | java | A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. | 2015 | mented in [java] and avail | |
| 25777525 | r | Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. | 2015 | dinal: an [R package] for stati | |
| 25765347 | r | ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. | 2015 | ker is an [R package] for annot | |
| 25755273 | java | BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. | 2015 | mented in [java] and c++, | |
| 25755273 | c++ | BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. | 2015 | java and [C++], to ident | |
| 25735769 | mathlab | Logical transformation of genome-scale metabolic models for gene level applications and analysis. | 2015 | mented in [matlab], raven to | |
| 25725498 | c++ | L-GRAAL: Lagrangian graphlet-based network aligner. | 2015 | coded in [C++]. software | |
| 25725494 | java | GeLL: a generalized likelihood library for phylogenetic models. | 2015 | t gell, a [java] library t | |
| 25725090 | r | SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. | 2015 | ed in the [R package] simseq, w | |
| 25717194 | c++ | Fast, accurate, and reliable molecular docking with QuickVina 2. | 2015 | the [C++] source co | |
| 25717189 | r | rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data. | 2015 | resent an [R package], rseqnp, | |
| 25712692 | r | specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. | 2015 | ed in the [R language] and avail | |
| 25707528 | c++ | PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. | 2015 | tandalone [C++] source co | |
| 25701576 | mathlab | Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study. | 2015 | the [matlab] code for | |
| 25701573 | java | Oasis: online analysis of small RNA deep sequencing data. | 2015 | ython, r, [java], php, c++ | |
| 25701573 | python | Oasis: online analysis of small RNA deep sequencing data. | 2015 | mented in [python], r, java, | |
| 25701573 | c++ | Oasis: online analysis of small RNA deep sequencing data. | 2015 | ava, php, [C++] and javas | |
| 25701573 | javascript | Oasis: online analysis of small RNA deep sequencing data. | 2015 | , c++ and [javascript]. it is fr | |
| 25686638 | java | RAPTR-SV: a hybrid method for the detection of structural variants. | 2015 | ritten in [java] and uses | |
| 25677125 | r | DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. | 2015 | ose is an [R package] providing | |
| 25673340 | python | MESMER: minimal ensemble solutions to multiple experimental restraints. | 2015 | , modular [python] plugins e | |
| 25667548 | c++ | A multiobjective memetic algorithm for PPI network alignment. | 2015 | the [C++] source co | |
| 25661541 | c++ | Whiteboard: a framework for the programmatic visualization of complex biological analyses. | 2015 | mented in [C++] that enab | |
| 25652236 | r | BACA: bubble chArt to compare annotations. | 2015 | le at the [CRAN] repositor | |
| 25649621 | python | Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. | 2015 | cation in [python], availabl | |
| 25644271 | perl | Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. | 2015 | mented in [perl] and is su | |
| 25644269 | r | ClassifyR: an R package for performance assessment of classification with applications to transcriptomics. | 2015 | sifyr: an [R package] for perfo | |
| 25644268 | r | CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data. | 2015 | from the [CRAN] repositor | |
| 25638814 | mathlab | Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions. | 2015 | the [matlab] source co | |
| 25638808 | r | TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. | 2015 | mma-r: an [R package] for predi | |
| 25638808 | mathlab | TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. | 2015 | original [matlab] code. the | |
| 25638391 | r | Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data. | 2015 | ed in the [R package] wavcluste | |
| 25637560 | python | Omics Pipe: a community-based framework for reproducible multi-omics data analysis. | 2015 | tandalone [python] package f | |
| 25637558 | java | Dizzy-Beats: a Bayesian evidence analysis tool for systems biology. | 2015 | graphical [java] bayesian | |
| 25627825 | mathlab | SFMetrics: an analysis tool for scanning force microscopy images of biomolecules. | 2015 | ng within [matlab] environme | |
| 25626999 | r | Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. | 2015 | using an [R package] that we h | |
| 25626688 | c++ | MDAT- Aligning multiple domain arrangements. | 2015 | coded in [C++], and the | |
| 25619996 | r | protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. | 2015 | protrweb: [R package] and web s | |
| 25619995 | c++ | Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics. | 2015 | he bia in [C++], along wi | |
| 25617415 | r | ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. | 2015 | ttp://www.[Bioconductor].org/packa | |
| 25609796 | r | dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis. | 2015 | slice: an [R package] for nonpa | |
| 25609794 | r | MethylMix: an R package for identifying DNA methylation-driven genes. | 2015 | ylmix: an [R package] for ident | |
| 25600654 | mathlab | Sample size calculation in metabolic phenotyping studies. | 2015 | rithm for [matlab] and gnu o | |
| 25592847 | r | Semi-supervised adaptive-height snipping of the hierarchical clustering tree. | 2015 | data sets [and R] code are | |
| 25591917 | mathlab | Predicting protein functions using incomplete hierarchical labels. | 2015 | bels. the [matlab] code of p | |
| 25591325 | javascript | YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. | 2015 | nchronous [javascript] and xml ( | |
| 25568282 | c++ | A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. | 2015 | d gtdt in [C++] and the s | |
| 25568279 | java | GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. | 2015 | ebserver, [java] applet, u | |
| 25563332 | r | Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. | 2015 | en-source [R package] htscluste | |
| 25550326 | r | PRSice: Polygenic Risk Score software. | 2015 | prsice is [written in R], includin | |
| 25550326 | bash | PRSice: Polygenic Risk Score software. | 2015 | ppers for [bash] data mana | |
| 25543048 | python | An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps. | 2015 | nt here a [python] library i | |
| 25540184 | java | J-Circos: an interactive Circos plotter. | 2015 | uses the [java] computer | |
| 25535243 | c++ | A Bayesian framework for de novo mutation calling in parents-offspring trios. | 2015 | the [C++] source co | |
| 25527832 | c++ | Population-based structural variation discovery with Hydra-Multi. | 2015 | ritten in [C++] and is fr | |
| 25524895 | java | VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. | 2015 | code in [java] and pytho | |
| 25524895 | python | VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. | 2015 | java and [python] along wit | |
| 25519981 | mathlab | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis. | 2014 | reliable [matlab] code for | |
| 25505095 | python | Epock: rapid analysis of protein pocket dynamics. | 2015 | rce code, [python] analysis | |
| 25505095 | c++ | Epock: rapid analysis of protein pocket dynamics. | 2015 | epock [C++] source co | |
| 25505094 | java | Detection of circular permutations within protein structures using CE-CP. | 2015 | s part of [biojava] 3 (http:/ | |
| 25505092 | python | NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. | 2015 | rsions of [python] and tcl/t | |
| 25505090 | java | 3Dmol.js: molecular visualization with WebGL. | 2015 | lugins or [java]. 3dmol.js | |
| 25505090 | javascript | 3Dmol.js: molecular visualization with WebGL. | 2015 | -oriented [javascript] library t | |
| 25505087 | java | Sputnik: ad hoc distributed computation. | 2015 | ng only a [java] runtime, | |
| 25504849 | java | MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory. | 2015 | mptheory [java] library: | |
| 25504849 | r | MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory. | 2015 | thematica [and R]. | |
| 25504849 | mathlab | MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory. | 2015 | , such as [matlab], gnu octa | |
| 25504848 | python | repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects. | 2015 | repdna: a [python] package t | |
| 25496126 | python | Kiwi: a tool for integration and visualization of network topology and gene-set analysis. | 2014 | able as a [python] package a | |
| 25495450 | r | MPAgenomics: an R package for multi-patient analysis of genomic markers. | 2014 | omics: an [R package] for multi | |
| 25494997 | perl | Masking as an effective quality control method for next-generation sequencing data analysis. | 2014 | ield. the [perl] script fo | |
| 25492550 | r | Identifying and quantifying metabolites by scoring peaks of GC-MS data. | 2014 | core in a [R package] called me | |
| 25491122 | python | MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. | 2014 | video and [python] source co | |
| 25491031 | r | Integrating protein structural dynamics and evolutionary analysis with Bio3D. | 2014 | dependent [R package] under a g | |
| 25490956 | r | Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. | 2014 | g matlab® [and R], allowing | |
| 25481010 | python | SNPlice: variants that modulate Intron retention from RNA-sequencing data. | 2015 | rs and as [python] source-co | |
| 25481009 | c++ | ICMA: an integrated cardiac modeling and analysis platform. | 2015 | mented in [C++] using ope | |
| 25481008 | r | flowCL: ontology-based cell population labelling in flow cytometry. | 2015 | e through [Bioconductor] (http://w | |
| 25480372 | r | Semiconductor sequencing: how many flows do you need? | 2015 | from the [CRAN] repositor | |
| 25465054 | java | VTBuilder: a tool for the assembly of multi isoform transcriptomes. | 2014 | mented in [java] and is av | |
| 25431350 | c | Meta-eQTL: a tool set for flexible eQTL meta-analysis. | 2014 | ive parts [written in C]. the soft | |
| 25431350 | r | Meta-eQTL: a tool set for flexible eQTL meta-analysis. | 2014 | utilities [written in R], with som | |
| 25431229 | r | An efficient algorithm to explore liquid association on a genome-wide scale. | 2014 | ttp://www.[Bioconductor].org . | |
| 25417205 | r | QuasR: quantification and annotation of short reads in R. | 2015 | grated in [Bioconductor] so that i | |
| 25417204 | r | Genomation: a toolkit to summarize, annotate and visualize genomic intervals. | 2015 | built an [R package], genomati | |
| 25417203 | python | Efficient searching and annotation of metabolic networks using chemical similarity. | 2015 | [python] files wil | |
| 25416747 | mathlab | Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. | 2015 | e mlrr in [matlab] is availa | |
| 25414364 | c++ | The Victor C++ library for protein representation and advanced manipulation. | 2015 | he victor [C++] library f | |
| 25413436 | r | A framework for generalized subspace pattern mining in high-dimensional datasets. | 2014 | e through [CRAN] (http://c | |
| 25398608 | python | SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. | 2015 | ritten in [python] and requi | |
| 25391397 | c++ | Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures. | 2015 | [C++] source co | |
| 25388151 | java | EVpedia: a community web portal for extracellular vesicles research. | 2015 | d in php, [java], mysql an | |
| 25380959 | python | PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments. | 2015 | ritten in [python] and runs | |
| 25380958 | r | Development of a robust classifier for quality control of reverse-phase protein arrays. | 2015 | percurve [R package], can be f | |
| 25380956 | c++ | TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm. | 2015 | mented in [C++] and inter | |
| 25378466 | r | flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. | 2015 | e through [Bioconductor] (http://m | |
| 25371478 | java | JAMSS: proteomics mass spectrometry simulation in Java. | 2015 | lation in [java]. | |
| 25371114 | r | Optimising parallel R correlation matrix calculations on gene expression data using MapReduce. | 2014 | ed on the [R package] rhipe, de | |
| 25371041 | r | Missing value imputation in high-dimensional phenomic data: imputable or not, and how? | 2014 | thods. an [R package] phenomei | |
| 25367050 | mathlab | A MATLAB tool for pathway enrichment using a topology-based pathway regulation score. | 2014 | a [matlab] tool for | |
| 25362092 | c++ | Mass spectrometry-based protein identification with accurate statistical significance assignment. | 2015 | mented in [C++] on a linu | |
| 25359893 | mathlab | eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways. | 2015 | the [matlab] source co | |
| 25359149 | java | CIG-P: Circular Interaction Graph for Proteomics. | 2014 | through a [java] based gui | |
| 25355790 | r | Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction. | 2015 | [R package] 'nsgp' is | |
| 25348213 | python | DIANA--algorithmic improvements for analysis of data-independent acquisition MS data. | 2015 | scala and [python] and avail | |
| 25344501 | c | iDoComp: a compression scheme for assembled genomes. | 2015 | docomp is [written in C] and can b | |
| 25344498 | c++ | Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs. | 2015 | ode for a [C++] implement | |
| 25344497 | javascript | Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization. | 2015 | wser is a [javascript] web appli | |
| 25344496 | java | MP-GeneticSynth: inferring biological network regulations from time series. | 2015 | ynth is a [java] tool for | |
| 25342065 | python | piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. | 2015 | ash, c++, [python], perl and | |
| 25342065 | c++ | piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. | 2015 | in bash, [C++], python, | |
| 25342065 | r | piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. | 2015 | hon, perl [and R]. pipipes | |
| 25342065 | bash | piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. | 2015 | mented in [bash], c++, pyt | |
| 25342065 | perl | piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. | 2015 | , python, [perl] and r. pi | |
| 25338717 | python | FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. | 2015 | licensed [python] 2.7 code | |
| 25336502 | perl | Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker. | 2015 | mented in [perl] and runs | |
| 25336500 | r | Statistical significance of variables driving systematic variation in high-dimensional data. | 2015 | ilable in [CRAN]. | |
| 25332377 | r | Seed: a user-friendly tool for exploring and visualizing microbial community data. | 2015 | . seed is [written in R] using the | |
| 25331652 | perl | SummonChimera infers integrated viral genomes with nucleotide precision from NGS data. | 2014 | mera is a [perl] program t | |
| 25322836 | python | Rcount: simple and flexible RNA-Seq read counting. | 2015 | s, useful [python] and r scr | |
| 25322836 | c++ | Rcount: simple and flexible RNA-Seq read counting. | 2015 | mented in [C++] using the | |
| 25322836 | r | Rcount: simple and flexible RNA-Seq read counting. | 2015 | ul python [and R] scripts a | |
| 25322835 | java | miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data. | 2015 | mented in [java], is avail | |
| 25319962 | mathlab | GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks. | 2015 | olbox for [matlab] (also ava | |
| 25301849 | java | NOVA: a software to analyze complexome profiling data. | 2015 | at least [java] 7 and run | |
| 25286921 | r | Chimera: a Bioconductor package for secondary analysis of fusion products. | 2014 | himera: a [Bioconductor] package f | |
| 25286920 | r | Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data. | 2015 | le on the [CRAN] and is ma | |
| 25273112 | java | MulRF: a software package for phylogenetic analysis using multi-copy gene trees. | 2015 | he gui in [java] swing. | |
| 25273112 | c++ | MulRF: a software package for phylogenetic analysis using multi-copy gene trees. | 2015 | mented in [C++] and the g | |
| 25273109 | java | KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. | 2015 | nted as a [java] cytoscape | |
| 25273108 | mathlab | Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments. | 2015 | mented in [matlab] r2011b. m | |
| 25273107 | perl | ExportAid: database of RNA elements regulating nuclear RNA export in mammals. | 2015 | mented in [perl], mysql, a | |
| 25273107 | javascript | ExportAid: database of RNA elements regulating nuclear RNA export in mammals. | 2015 | pache and [javascript] with all | |
| 25273104 | r | WhopGenome: high-speed access to whole-genome variation and sequence data in R. | 2015 | hopgenome [R package] is availa | |
| 25273102 | python | A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature. | 2015 | a [python] package f | |
| 25267467 | r | DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. | 2014 | hecker: a [Bioconductor] package f | |
| 25266225 | python | GLAD: a mixed-membership model for heterogeneous tumor subtype classification. | 2015 | a [python] module im | |
| 25266224 | c++ | Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance. | 2015 | mented in [C++] with sour | |
| 25265915 | python | Polyphony: superposition independent methods for ensemble-based drug discovery. | 2014 | oded in a [python] package c | |
| 25262154 | r | Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. | 2015 | ly in the [R language]. it can b | |
| 25262153 | r | switchBox: an R package for k-Top Scoring Pairs classifier development. | 2015 | chbox: an [R package] for k-top | |
| 25260700 | python | HTSeq--a Python framework to work with high-throughput sequencing data. | 2015 | htseq--a [python] framework | |
| 25260699 | r | EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. | 2015 | the [R package] easystrat | |
| 25260628 | r | DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. | 2014 | iscml: an [R package] for estim | |
| 25252999 | c++ | Ensemble analysis of adaptive compressed genome sequencing strategies. | 2014 | mbler 2.0 [C++] source co | |
| 25246431 | mathlab | NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. | 2015 | mented in [matlab], runs on | |
| 25246429 | r | Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. | 2015 | from the [Bioconductor] site (htt | |
| 25236458 | r | Using population data for assessing next-generation sequencing performance. | 2015 | sing perl [and R] can be fo | |
| 25236458 | perl | Using population data for assessing next-generation sequencing performance. | 2015 | ion using [perl] and r can | |
| 25212756 | r | UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. | 2015 | conductor [R package] for unsup | |
| 25212755 | java | cddApp: a Cytoscape app for accessing the NCBI conserved domain database. | 2015 | ritten in [java] and freel | |
| 25202135 | r | Performance evaluation of DNA copy number segmentation methods. | 2015 | -platform [R package] jointseg, | |
| 25192743 | r | Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. | 2015 | [R package] and sourc | |
| 25192741 | python | BalestraWeb: efficient online evaluation of drug-target interactions. | 2015 | ted using [python], flask, n | |
| 25189781 | r | subSeq: determining appropriate sequencing depth through efficient read subsampling. | 2014 | he subseq [R package], which us | |
| 25176396 | javascript | jvenn: an interactive Venn diagram viewer. | 2014 | is a new [javascript] library. | |
| 25173419 | r | poRe: an R package for the visualization and analysis of nanopore sequencing data. | 2015 | pore: an [R package] for the v | |
| 25165095 | c++ | LoRDEC: accurate and efficient long read error correction. | 2014 | ritten in [C++], tested o | |
| 25165094 | perl | MIRPIPE: quantification of microRNAs in niche model organisms. | 2014 | mented in [perl] and integ | |
| 25165093 | perl | MR_predictor: a simulation engine for Mendelian Randomization studies. | 2014 | mented in [perl], and the | |
| 25161255 | r | Fast randomization of large genomic datasets while preserving alteration counts. | 2014 | loped the [R package] birewire, | |
| 25161251 | python | Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images. | 2014 | mented in [python] and makes | |
| 25161247 | mathlab | Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. | 2014 | our [matlab] implement | |
| 25161243 | c++ | RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. | 2014 | mented in [C++] as a stan | |
| 25161242 | c++ | Polytomy refinement for the correction of dubious duplications in gene trees. | 2014 | the [C++] source co | |
| 25161235 | mathlab | Causal network inference using biochemical kinetics. | 2014 | [matlab] r2014a so | |
| 25161225 | r | Broad-Enrich: functional interpretation of large sets of broad genomic regions. | 2014 | rsion and [R package]. | |
| 25161224 | r | Two-dimensional segmentation for analyzing Hi-C data. | 2014 | he hicseg [R package] is availa | |
| 25161219 | c++ | Lambda: the local aligner for massive biological data. | 2014 | en-source [C++] library f | |
| 25158845 | perl | APTE: identification of indirect read-out A-DNA promoter elements in genomes. | 2014 | a [perl] program ( | |
| 25152233 | perl | ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO. | 2014 | mented in [perl], php, r, | |
| 25150250 | python | ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. | 2014 | mented in [python] 2.7, usin | |
| 25150247 | c++ | Cosi2: an efficient simulator of exact and approximate coalescent with selection. | 2014 | a free [C++] implement | |
| 25147360 | javascript | Visualization of protein sequence features using JavaScript and SVG with pViz.js. | 2014 | res using [javascript] and svg w | |
| 25147359 | python | PyBamView: a browser-based application for viewing short read alignments. | 2014 | standard [python] package. | |
| 25147358 | r | MethylAid: visual and interactive quality control of large Illumina 450k datasets. | 2014 | kage (www.[Bioconductor].org/packa | |
| 25143291 | python | Poretools: a toolkit for analyzing nanopore sequence data. | 2014 | ritten in [python] as both a | |
| 25123905 | python | SCDFinder, a web-based tool for the identification of putative novel ATM and ATR targets. | 2014 | pearl and [python], and is a | |
| 25123902 | c++ | Cross-validation under separate sampling: strong bias and how to correct it. | 2014 | e code in [C++], along wi | |
| 25123900 | python | READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data. | 2014 | mented in [python] and is pu | |
| 25123899 | r | NetComm: a network analysis tool based on communicability. | 2014 | hod as an [R package] for use i | |
| 25115706 | python | Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes. | 2014 | in c and [python] and is su | |
| 25100686 | c++ | MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. | 2014 | ritten in [C++] with open | |
| 25095879 | python | Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. | 2014 | in r and [python], and sour | |
| 25086004 | r | Bias correction for selecting the minimal-error classifier from many machine learning models. | 2014 | uracy. an [R package] 'mlbias' | |
| 25078398 | r | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data. | 2014 | ttp://www.[Bioconductor].org/. a v | |
| 25077818 | java | Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications. | 2014 | n for the [java] programmi | |
| 25075120 | r | NetPathMiner: R/Bioconductor package for network path mining through gene expression. | 2014 | e through [Bioconductor] and from | |
| 25075118 | c++ | FARVAT: a family-based rare variant association test. | 2014 | mented in [C++], and appl | |
| 25075116 | c++ | Trowel: a fast and accurate error correction module for Illumina sequencing reads. | 2014 | ritten in [C++] and is pr | |
| 25075114 | r | Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data. | 2014 | omxtr: an [R package] for mixtu | |
| 25075113 | perl | Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG. | 2014 | ator is a [perl] applicati | |
| 25066046 | mathlab | Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems. | 2014 | ases. the [matlab] sources i | |
| 25064568 | perl | e-Driver: a novel method to identify protein regions driving cancer. | 2014 | a [perl] script wi | |
| 25064564 | c++ | Compression and fast retrieval of SNP data. | 2014 | nted in a [C++] library, | |
| 25061071 | r | FisHiCal: an R package for iterative FISH-based calibration of Hi-C data. | 2014 | hical: an [R package] for itera | |
| 25061070 | python | STAMP: statistical analysis of taxonomic and functional profiles. | 2014 | gnu gpl. [python] source co | |
| 25061069 | mathlab | Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data. | 2014 | the r and [matlab] scripts a | |
| 25061068 | r | Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. | 2014 | mitted to [Bioconductor]. | |
| 25053745 | r | sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. | 2014 | nted as a [Bioconductor] package i | |
| 25035399 | r | lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R. | 2014 | stry. our [R package], lrgpr, a | |
| 25028724 | r | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow. | 2014 | s) and an [R package] (snpolish | |
| 25012182 | r | repfdr: a tool for replicability analysis for genome-wide association studies. | 2014 | the [R package] repfdr pr | |
| 25005023 | perl | Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes. | 2014 | mand line [perl] script fr | |
| 25004928 | r | A test for comparing two groups of samples when analyzing multiple omics profiles. | 2014 | rt of the [Bioconductor] package s | |
| 24994891 | mathlab | FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. | 2014 | ndpath: a [matlab] solution | |
| 24990767 | r | A spatial simulation approach to account for protein structure when identifying non-random somatic mutations. | 2014 | alk. the [R package] is availa | |
| 24990606 | r | Intensity drift removal in LC/MS metabolomics by common variance compensation. | 2014 | le as the [R package] intcor at | |
| 24990605 | java | ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. | 2014 | [java] source an | |
| 24990604 | r | RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy. | 2014 | en-source [R package] that impl | |
| 24990603 | c++ | GATB: Genome Assembly & Analysis Tool Box. | 2014 | ritten in [C++] and is av | |
| 24982428 | python | COSMOS: Python library for massively parallel workflows. | 2014 | cosmos: [python] library f | |
| 24974206 | r | bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). | 2014 | s/. it is [using R] (http://w | |
| 24974204 | python | Learning protein-DNA interaction landscapes by integrating experimental data through computational models. | 2014 | mpete and [python] source co | |
| 24966365 | bash | H3M2: detection of runs of homozygosity from whole-exome sequencing data. | 2014 | ection of [bash], r and fo | |
| 24966365 | fortran | H3M2: detection of runs of homozygosity from whole-exome sequencing data. | 2014 | sh, r and [fortran] scripts a | |
| 24965054 | mathlab | Ycasd - a tool for capturing and scaling data from graphical representations. | 2014 | tted as a [matlab] or an r m | |
| 24947750 | c++ | Omega: an overlap-graph de novo assembler for metagenomics. | 2014 | mented in [C++] with sour | |
| 24939150 | python | DAFGA: diversity analysis of functional gene amplicons. | 2014 | veloped a [python] script pa | |
| 24938393 | r | CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data. | 2014 | mented an [R package] called ci | |
| 24938393 | perl | CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data. | 2014 | 2009), a [perl] script, i | |
| 24932009 | python | Pareto-optimal phylogenetic tree reconciliation. | 2014 | our [python] tools are | |
| 24932008 | python | A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. | 2014 | [python] and matla | |
| 24932008 | mathlab | A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. | 2014 | ython and [matlab] implement | |
| 24931999 | java | Stochastic EM-based TFBS motif discovery with MITSU. | 2014 | [java] executabl | |
| 24931992 | python | A statistical approach for inferring the 3D structure of the genome. | 2014 | a [python] implement | |
| 24931977 | c++ | Graph-regularized dual Lasso for robust eQTL mapping. | 2014 | for both [C++] version a | |
| 24931977 | mathlab | Graph-regularized dual Lasso for robust eQTL mapping. | 2014 | rsion and [matlab] version i | |
| 24931973 | r | Cross-study validation for the assessment of prediction algorithms. | 2014 | e through [Bioconductor]. | |
| 24930143 | mathlab | LICRE: unsupervised feature correlation reduction for lipidomics. | 2014 | the [matlab] implement | |
| 24930138 | java | The Scramble conversion tool. | 2014 | ion is in [java]. we prese | |
| 24930009 | r | Determination of sample size for a multi-class classifier based on single-nucleotide polymorphisms: a volume under the surface approach. | 2014 | anual for [R package] samplesi | |
| 24929920 | perl | An integrative method to normalize RNA-Seq data. | 2014 | ritten in [perl] and avail | |
| 24928209 | r | NetBioV: an R package for visualizing large network data in biology and medicine. | 2014 | tbiov: an [R package] for visua | |
| 24925766 | python | L.U.St: a tool for approximated maximum likelihood supertree reconstruction. | 2014 | ackage, a [python] tool for | |
| 24915860 | mathlab | Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm. | 2014 | ripted in [matlab] (mathwork | |
| 24913447 | c++ | SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations. | 2014 | coded in [C++] and is he | |
| 24909518 | java | MiningABs: mining associated biomarkers across multi-connected gene expression datasets. | 2014 | reatment. [java] source co | |
| 24907369 | java | ABRA: improved coding indel detection via assembly-based realignment. | 2014 | nation of [java] and c/c++ | |
| 24907368 | r | Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. | 2014 | performed [using R] version 2 | |
| 24907367 | r | MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. | 2014 | hp), perl [and R]. it is fr | |
| 24907367 | perl | MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. | 2014 | or (php), [perl] and r. it | |
| 24907367 | javascript | MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. | 2014 | e node.js [javascript] framework | |
| 24906803 | c++ | hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. | 2014 | mented in [C++] and paral | |
| 24906803 | r | hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. | 2014 | phase: an [R package] for pedig | |
| 24903420 | r | Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. | 2014 | ushi) and [Bioconductor] (http://b | |
| 24903419 | r | Gene set analysis: limitations in popular existing methods and proposed improvements. | 2014 | ilable as [R package] from cran | |
| 24894503 | r | Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. | 2014 | pro is an [R package] specifica | |
| 24886250 | r | KRLMM: an adaptive genotype calling method for common and low frequency variants. | 2014 | d via the [Bioconductor] project ( | |
| 24886202 | r | An R package that automatically collects and archives details for reproducible computing. | 2014 | an [R package] that auto | |
| 24885957 | python | MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. | 2014 | ilable in [python] via a wra | |
| 24885957 | r | MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. | 2014 | uded. the [R package] has been | |
| 24885957 | mathlab | MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. | 2014 | an r and [matlab] optimizat | |
| 24885091 | java | BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data. | 2014 | nted as a [java] applicati | |
| 24884810 | python | GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. | 2014 | erl, r or [python]. the outp | |
| 24884810 | perl | GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. | 2014 | s such as [perl], r or pyt | |
| 24876377 | r | PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. | 2014 | cnv/, and [R package] at https: | |
| 24876377 | perl | PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. | 2014 | ted using [perl] and r, an | |
| 24876375 | java | CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. | 2014 | ritten in [java]. binaries | |
| 24872424 | java | CODOC: efficient access, analysis and compression of depth of coverage signals. | 2014 | [java] source co | |
| 24867942 | c++ | keeSeek: searching distant non-existing words in genomes for PCR-based applications. | 2014 | mented in [C++] and cuda | |
| 24867941 | python | MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. | 2014 | ompanying [python] scripts a | |
| 24867941 | c++ | MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. | 2014 | mented in [C++]. source c | |
| 24860160 | perl | Identification of chromosomal translocation hotspots via scan statistics. | 2014 | in r and [perl]. source c | |
| 24860159 | java | GenomeVISTA--an integrated software package for whole-genome alignment and visualization. | 2014 | c/c++ and [java], the sour | |
| 24860159 | perl | GenomeVISTA--an integrated software package for whole-genome alignment and visualization. | 2014 | mented in [perl], c/c++ an | |
| 24849580 | mathlab | Accurate cell segmentation in microscopy images using membrane patterns. | 2014 | [matlab] code and | |
| 24849579 | c++ | MaxLink: network-based prioritization of genes tightly linked to a disease seed set. | 2014 | tation in [C++], and the | |
| 24836530 | r | MethylSig: a whole genome DNA methylation analysis pipeline. | 2014 | ble as an [R package] at http:/ | |
| 24833804 | c++ | Memory-efficient RNA energy landscape exploration. | 2014 | rt of the [C++] energy la | |
| 24828656 | c++ | Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison. | 2014 | mented in [C++], and the | |
| 24825614 | java | PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. | 2014 | mented in [java], with vis | |
| 24825612 | python | PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy. | 2014 | the [python] source co | |
| 24813215 | r | compcodeR--an R package for benchmarking differential expression methods for RNA-seq data. | 2014 | coder--an [R package] for bench | |
| 24813214 | r | Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. | 2014 | ble as an [R package] from the | |
| 24812342 | mathlab | PhenoNet: identification of key networks associated with disease phenotype. | 2014 | [matlab] code is a | |
| 24812338 | r | RNASeqGUI: a GUI for analysing RNA-Seq data. | 2014 | rnaseqgui [R package], a graphi | |
| 24812337 | mathlab | SEK: sparsity exploiting k-mer-based estimation of bacterial community composition. | 2014 | dependent [matlab] implement | |
| 24794933 | r | unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R. | 2014 | veloped a [Bioconductor] package f | |
| 24794931 | r | MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. | 2014 | stats: an [R package] for stati | |
| 24794927 | c++ | A fast and powerful tree-based association test for detecting complex joint effects in case-control studies. | 2014 | mented in [C++] and r and | |
| 24794927 | r | A fast and powerful tree-based association test for detecting complex joint effects in case-control studies. | 2014 | ed in c++ [and R] and suppo | |
| 24778109 | fortran | Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway. | 2014 | [fortran] codes for | |
| 24771560 | java | WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. | 2014 | mented in [java] and javas | |
| 24771560 | javascript | WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. | 2014 | java and [javascript] using the | |
| 24764462 | r | On non-detects in qPCR data. | 2014 | ed in the [R package], nondetec | |
| 24764461 | python | relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. | 2014 | ritten in [python] with c mo | |
| 24764459 | r | kdetrees: Non-parametric estimation of phylogenetic tree distributions. | 2014 | ed as the [R package] kdetrees | |
| 24755303 | r | A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data. | 2014 | an [R package] 'rvsel' c | |
| 24753490 | r | Rgb: a scriptable genome browser for R. | 2014 | data, no [R package] currently | |
| 24753486 | r | aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. | 2014 | alfq is [written in R] and freel | |
| 24747219 | python | DSRC 2--Industry-oriented compression of FASTQ files. | 2014 | or, c and [python] libraries | |
| 24740360 | r | Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. | 2014 | es of the [R package] rvsharing | |
| 24733291 | r | R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. | 2014 | this [R package] is freely | |
| 24728858 | java | A change-point model for identifying 3'UTR switching by next-generation RNA sequencing. | 2014 | mented in [java] and can b | |
| 24728855 | r | geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. | 2014 | e popular [R package] geiger. w | |
| 24728852 | mathlab | Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. | 2014 | [matlab] code is p | |
| 24675730 | r | CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. | 2014 | lorer: an [R package] for the a | |
| 24403538 | python | Allerdictor: fast allergen prediction using text classification techniques. | 2014 | mented in [python] and avail | |
| 24395754 | r | QCGWAS: A flexible R package for automated quality control of genome-wide association results. | 2014 | flexible [R package] for autom | |
| 24389661 | r | AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. | 2014 | the [R package] abscnseq | |
| 24389660 | c | Estimation of fluorescence-tagged RNA numbers from spot intensities. | 2014 | xtensions [written in C] for param | |
| 24389660 | mathlab | Estimation of fluorescence-tagged RNA numbers from spot intensities. | 2014 | [matlab] extension | |
| 24389657 | python | Bias from removing read duplication in ultra-deep sequencing experiments. | 2014 | a [python] implement | |
| 24371153 | r | SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. | 2014 | nted in c [and R] and are p | |
| 24712852 | java | TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens. | 2014 | lysis), a [java] and r-bas | |
| 24711652 | python | Filling annotation gaps in yeast genomes using genome-wide contact maps. | 2014 | with the [python] code and | |
| 24700319 | r | rTANDEM, an R/Bioconductor package for MS/MS protein identification. | 2014 | ssociated [R package], shinytan | |
| 24695406 | python | Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. | 2014 | ritten in [python] and is pu | |
| 24681909 | r | flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies. | 2014 | lowfit: a [Bioconductor] package t | |
| 24681908 | c++ | molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. | 2014 | le as gpl [C++] source co | |
| 24681907 | r | VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. | 2014 | tation: a [Bioconductor] package f | |
| 24681904 | r | CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure. | 2014 | mut is an [R package] designed | |
| 24681903 | java | Census 2: isobaric labeling data analysis. | 2014 | requires [java] version 6 | |
| 24678608 | r | Differential meta-analysis of RNA-seq data from multiple studies. | 2014 | fects. an [R package] metarnase | |
| 24669769 | r | A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. | 2014 | hods. the [R package] is availa | |
| 24669753 | python | FreeContact: fast and free software for protein contact prediction from residue co-evolution. | 2014 | perl and [python] modules. | |
| 24669753 | c++ | FreeContact: fast and free software for protein contact prediction from residue co-evolution. | 2014 | the free [C++] library | |
| 24669753 | perl | FreeContact: fast and free software for protein contact prediction from residue co-evolution. | 2014 | s well as [perl] and pytho | |
| 24659106 | c++ | Improved transcript isoform discovery using ORF graphs. | 2014 | ilable as [C++] source co | |
| 24659105 | r | massiR: a method for predicting the sex of samples in gene expression microarray datasets. | 2014 | nted as a [Bioconductor] package i | |
| 24659032 | r | TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception. | 2014 | an [R package] implement | |
| 24655717 | r | spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. | 2014 | licer: an [R package] for class | |
| 24651968 | python | tqDist: a library for computing the quartet and triplet distances between binary or general trees. | 2014 | er with a [python] module an | |
| 24651968 | r | tqDist: a library for computing the quartet and triplet distances between binary or general trees. | 2014 | le and an [R package] for scrip | |
| 24650281 | python | The characteristic direction: a geometrical approach to identify differentially expressed genes. | 2014 | uages: r, [python], matlab a | |
| 24650281 | mathlab | The characteristic direction: a geometrical approach to identify differentially expressed genes. | 2014 | , python, [matlab] and mathe | |
| 24648041 | c++ | Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. | 2014 | mented in [C++] as standa | |
| 24646301 | perl | ShatterProof: operational detection and quantification of chromothripsis. | 2014 | ://search.[CPAN].org/~sgov | |
| 24642064 | java | KAnalyze: a fast versatile pipelined k-mer toolkit. | 2014 | mented in [java] 7, and th | |
| 24642064 | perl | KAnalyze: a fast versatile pipelined k-mer toolkit. | 2014 | built on [perl] and linux | |
| 24642063 | perl | Prokka: rapid prokaryotic genome annotation. | 2014 | mented in [perl] and is fr | |
| 24642062 | mathlab | Piecewise-constant and low-rank approximation for identification of recurrent copy number variations. | 2014 | the [matlab] code is a | |
| 24642061 | r | An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). | 2014 | an [R package] to analys | |
| 24632499 | mathlab | A general method for accurate estimation of false discovery rates in identification of differentially expressed genes. | 2014 | mented in [matlab] and is av | |
| 24632498 | perl | FSuite: exploiting inbreeding in dense SNP chip and exome data. | 2014 | eloped in [perl] and uses | |
| 24618474 | mathlab | Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach. | 2014 | data and [matlab] source co | |
| 24618468 | r | Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data. | 2014 | s part of [Bioconductor] at www.bi | |
| 24618465 | java | A personalized committee classification approach to improving prediction of breast cancer metastasis. | 2014 | atlab and [java] available | |
| 24618465 | mathlab | A personalized committee classification approach to improving prediction of breast cancer metastasis. | 2014 | mented in [matlab] and java | |
| 24618464 | java | The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. | 2014 | mented in [java] and makes | |
| 24618464 | perl | The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. | 2014 | java and [perl]. the tool | |
| 24618463 | java | A gradient-boosting approach for filtering de novo mutations in parent-offspring trios. | 2014 | nation of [java] and r is | |
| 24618463 | r | A gradient-boosting approach for filtering de novo mutations in parent-offspring trios. | 2014 | n of java [and R] is freely | |
| 24618462 | perl | The Bio-Community Perl toolkit for microbial ecology. | 2014 | community [perl] toolkit f | |
| 24603986 | r | Estimating optimal window size for analysis of low-coverage next-generation sequence data. | 2014 | an [R package] to estima | |
| 24603985 | python | PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. | 2014 | ritten in [python] and freel | |
| 24590441 | mathlab | Protein fold recognition using geometric kernel data fusion. | 2014 | the [matlab] code used | |
| 24585771 | python | Wrangling Galaxy's reference data. | 2014 | mented in [python] and has b | |
| 24578404 | perl | Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. | 2014 | the [perl] source co | |
| 24574115 | java | BioPlat: a software for human cancer biomarker discovery. | 2014 | mented in [java] and suppo | |
| 24567545 | c++ | iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array. | 2014 | mented in [C++] for use o | |
| 24567544 | javascript | jHeatmap: an interactive heatmap viewer for the web. | 2014 | adaptable [javascript] library d | |
| 24564732 | r | The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. | 2014 | ilable in [Bioconductor] for subse | |
| 24564706 | python | Finishing bacterial genome assemblies with Mix. | 2013 | mented in [python] and is av | |
| 24564704 | java | Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes. | 2013 | the [java] codes are | |
| 24564437 | mathlab | HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening. | 2013 | nloadable [matlab] project a | |
| 24564336 | mathlab | ProphNet: a generic prioritization method through propagation of information. | 2014 | ophnet. a [matlab] implement | |
| 24564231 | r | Efficient digest of high-throughput sequencing data in a reproducible report. | 2013 | uses the [R language] and bioco | |
| 24558116 | c | MRHMMs: multivariate regression hidden Markov models and the variantS. | 2014 | ftware is [written in C] for the s | |
| 24555693 | r | Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis. | 2014 | eloped an [R package] mseapca | |
| 24554630 | mathlab | Automated analysis of giant unilamellar vesicles using circular Hough transformation. | 2014 | mented in [matlab] (the math | |
| 24535097 | r | SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing. | 2014 | eqgsea: a [Bioconductor] package f | |
| 24532724 | r | ADaCGH2: parallelized analysis of (big) CNA data. | 2014 | gh2 is an [R package] available | |
| 24532722 | c++ | fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. | 2014 | ritten in [C++] using ope | |
| 24532720 | r | LPmerge: an R package for merging genetic maps by linear programming. | 2014 | merge: an [R package] for mergi | |
| 24532718 | python | TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. | 2014 | tssv as a [python] package t | |
| 24519380 | r | An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function. | 2014 | r work an [R package] giving ac | |
| 24511080 | python | HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. | 2014 | mented in [python], and sour | |
| 24501098 | r | Visualization and probability-based scoring of structural variants within repetitive sequences. | 2014 | hod as an [R package] available | |
| 24499370 | r | Mining locus tags in PubMed Central to improve microbial gene annotation. | 2014 | eloped an [R package] called pm | |
| 24499321 | c++ | Improving read mapping using additional prefix grams. | 2014 | mented in [C++], and the | |
| 24497503 | python | AMASS: a database for investigating protein structures. | 2014 | nted with [biopython] and apach | |
| 24493035 | perl | ARTS: automated randomization of multiple traits for study design. | 2014 | mented in [perl] and is av | |
| 24489371 | c++ | StochHMM: a flexible hidden Markov model tool and C++ library. | 2014 | tool and [C++] library. | |
| 24489369 | r | Comparing DNA integration site clusters with scan statistics. | 2014 | rxcluster [R package] containin | |
| 24489367 | mathlab | Bayesian joint analysis of heterogeneous genomics data. | 2014 | ritten in [matlab] and has b | |
| 24478339 | r | Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. | 2014 | rehensive [Bioconductor] package f | |
| 24470576 | bash | NGSANE: a lightweight production informatics framework for high-throughput data analysis. | 2014 | rom linux [bash] commands | |
| 24470574 | python | PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. | 2014 | mented in [python] and c++. | |
| 24470574 | c++ | PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. | 2014 | ython and [C++]. it bundl | |
| 24458951 | r | The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression. | 2014 | the oasis [R package] at http:/ | |
| 24451629 | r | h5vc: scalable nucleotide tallies with HDF5. | 2014 | rough the [Bioconductor] project. | |
| 24451624 | r | CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. | 2014 | cafe: an [R package] for the d | |
| 24451622 | r | Reference-free cell mixture adjustments in analysis of DNA methylation data. | 2014 | le in the [R package] reffreeew | |
| 24447369 | mathlab | Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. | 2014 | he genes. [matlab] code with | |
| 24444459 | java | BioShell-Threading: versatile Monte Carlo package for protein 3D threading. | 2014 | a set of [java] classes c | |
| 24443383 | r | ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. | 2014 | metab: an [R package] for bayes | |
| 24428888 | r | OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer. | 2014 | using the ['R'] algorithm | |
| 24423115 | python | kruX: matrix-based non-parametric eQTL discovery. | 2014 | n matlab, [python] and r tha | |
| 24423115 | r | kruX: matrix-based non-parametric eQTL discovery. | 2014 | b, python [and R] that uses | |
| 24423115 | mathlab | kruX: matrix-based non-parametric eQTL discovery. | 2014 | mented in [matlab], python a | |
| 24407226 | r | Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data. | 2014 | ptimyx: a [Bioconductor] pipeline | |
| 24371154 | c++ | MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. | 2014 | sensor, a [C++] program f | |
| 24363381 | perl | SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization. | 2014 | mented in [perl] and c/c++ | |
| 24363379 | java | Ondex Web: web-based visualization and exploration of heterogeneous biological networks. | 2014 | ritten in [java] and can b | |
| 24363378 | python | SplicePlot: a utility for visualizing splicing quantitative trait loci. | 2014 | mented in [python] and is su | |
| 24363376 | java | JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. | 2014 | mented in [java] and multi | |
| 24363375 | c++ | GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU. | 2014 | ture) and [C++]. source c | |
| 24359123 | c++ | A comparison study of succinct data structures for use in GWAS. | 2013 | veloped a [C++] library, | |
| 24351709 | python | CrossMap: a versatile tool for coordinate conversion between genome assemblies. | 2014 | ritten in [python] and c. so | |
| 24351708 | mathlab | Wigwams: identifying gene modules co-regulated across multiple biological conditions. | 2014 | a [matlab] implement | |
| 24336808 | java | ProbeSelect: selecting differentially expressed probes in transcriptional profile data. | 2014 | mented in [java] and avail | |
| 24336807 | mathlab | ORCA: a COBRA toolbox extension for model-driven discovery and analysis. | 2014 | t orca, a [matlab] package, | |
| 24336642 | r | ChAMP: 450k Chip Analysis Methylation Pipeline. | 2014 | nted as a [Bioconductor] package i | |
| 24336414 | c++ | BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. | 2014 | s in leda [C++], experime | |
| 24336146 | c++ | forqs: forward-in-time simulation of recombination, quantitative traits and selection. | 2014 | mand-line [C++] program. | |
| 24330312 | r | Marmal-aid--a database for Infinium HumanMethylation450. | 2013 | using an [R package] to allow | |
| 24308302 | python | Processing genome scale tabular data with wormtable. | 2013 | r data in [python]. wormtabl | |
| 24307704 | r | Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. | 2014 | hod in an [R package] called se | |
| 24307703 | r | Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network. | 2014 | ascade: a [R package] to study, | |
| 24267918 | java | An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets. | 2013 | sion. the [java] source co | |
| 24297519 | mathlab | Topological augmentation to infer hidden processes in biological systems. | 2014 | [matlab] code and | |
| 24292941 | java | AISAIC: a software suite for accurate identification of significant aberrations in cancers. | 2014 | escribe a [java] aisaic pa | |
| 24292937 | r | Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. | 2014 | atistical [language r]. code and | |
| 24281695 | c++ | Flexible analysis of RNA-seq data using mixed effects models. | 2014 | ithreaded [C++] programs | |
| 24273246 | java | Sequence alignment visualization in HTML5 without Java. | 2014 | 5 without [java]. | |
| 24273246 | javascript | Sequence alignment visualization in HTML5 without Java. | 2014 | html and [javascript] for inter | |
| 24273242 | c++ | jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework. | 2014 | ms with a [C++] metaheuri | |
| 24273239 | python | Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. | 2014 | the [python] analysis | |
| 24266924 | python | zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. | 2013 | hmm, with [python] bindings | |
| 24266924 | c++ | zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. | 2013 | ithm as a [C++] library, | |
| 24257187 | mathlab | Effect of separate sampling on classification accuracy. | 2014 | ritten in [matlab]. a functi | |
| 24257186 | mathlab | FastPros: screening of reaction knockout strategies for metabolic engineering. | 2014 | mented in [matlab] and cobra | |
| 24256072 | r | A novel phenotypic dissimilarity method for image-based high-throughput screens. | 2013 | ble as an [R package]. | |
| 24255646 | r | Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. | 2014 | the [R package] abs filte | |
| 24243934 | java | ASSIST: a fast versatile local structural comparison tool. | 2014 | eloped in [java] se 6, wit | |
| 24234003 | perl | footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. | 2014 | ed in php,[perl], mysql an | |
| 24229408 | c++ | SUNPLIN: simulation with uncertainty for phylogenetic investigations. | 2013 | en in the [C++] language. | |
| 24227677 | r | featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. | 2014 | ttp://www.[Bioconductor].org) soft | |
| 24227674 | r | MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. | 2014 | antage of [Bioconductor]'s annotat | |
| 24222209 | r | tRanslatome: an R/Bioconductor package to portray translational control. | 2014 | ilable in [Bioconductor]. | |
| 24215025 | r | RelateAdmix: a software tool for estimating relatedness between admixed individuals. | 2014 | nted in c [and R], is freel | |
| 24192544 | perl | WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. | 2014 | plemented [perl]. | |
| 24192544 | mathlab | WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. | 2014 | mented in [matlab], and copy | |
| 24191071 | javascript | Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. | 2014 | that uses [javascript] to genera | |
| 24191069 | r | Model-based clustering for RNA-seq data. | 2014 | an [R package], mbcluste | |
| 24177721 | python | AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. | 2014 | coded in [python], and is a | |
| 24177720 | mathlab | MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. | 2014 | tworks in [matlab] using mai | |
| 24177716 | python | pyGCluster, a novel hierarchical clustering approach. | 2014 | requires [python] 2.7, it i | |
| 24174567 | r | MSPrep--summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. | 2014 | he msprep [R package] to comple | |
| 24167158 | r | Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. | 2014 | the [R package] 'directpa | |
| 24167156 | python | AllergenFP: allergenicity prediction by descriptor fingerprints. | 2014 | ritten in [python], with giu | |
| 24162561 | r | Discriminative motif analysis of high-throughput dataset. | 2014 | e via the [Bioconductor] repositor | |
| 24162467 | r | Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data. | 2014 | ted in an [R package], which is | |
| 24152242 | java | Compact representation of k-mer de Bruijn graphs for genome read assembly. | 2013 | reads. a [java] implement | |
| 24149054 | java | SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. | 2014 | adoop and [java], they are | |
| 24149052 | java | BEReX: Biomedical Entity-Relationship eXplorer. | 2014 | tandalone [java] applicati | |
| 24149051 | r | Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems. | 2014 | butterfly [R package]. in the i | |
| 24135265 | r | A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. | 2014 | ttp://www.[Bioconductor].org/packa | |
| 24135262 | mathlab | Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. | 2014 | en-source [matlab] toolbox g | |
| 24132929 | r | gCMAP: user-friendly connectivity mapping with R. | 2014 | ystems at [Bioconductor] (http://w | |
| 24130306 | java | SecStAnT: secondary structure analysis tool for data selection, statistics and models building. | 2014 | mented in [java] and suppo | |
| 24123675 | java | GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads. | 2014 | mented in [java] and is av | |
| 24123674 | mathlab | PLIDA: cross-platform gene expression normalization using perturbed topic models. | 2014 | [matlab] code is a | |
| 24123673 | r | Two novel pathway analysis methods based on a hierarchical model. | 2014 | an [R package] is under | |
| 24115169 | c++ | A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes. | 2014 | mented in [C++] with open | |
| 24112435 | java | cudaMap: a GPU accelerated program for gene expression connectivity mapping. | 2013 | a popular [java] applicati | |
| 24108186 | java | The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. | 2014 | oviding a [java] library, | |
| 24098943 | c++ | Advances in the REDCAT software package. | 2013 | oriented [C++] environme | |
| 24085566 | mathlab | MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. | 2014 | mented in [matlab] is public | |
| 24078713 | r | ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses. | 2013 | gtools, a [Bioconductor] package, | |
| 24078702 | javascript | STAR: an integrated solution to management and visualization of sequencing data. | 2013 | leverages [javascript], html5 ca | |
| 24078685 | java | Lep-MAP: fast and accurate linkage map construction for large SNP datasets. | 2013 | [java] source co | |
| 24072732 | java | WebGLORE: a web service for Grid LOgistic REgression. | 2013 | tes ajax, [java] applet/se | |
| 24068035 | java | BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. | 2013 | teractive [java] program f | |
| 24064421 | r | Methods and challenges in timing chromosomal abnormalities within cancer samples. | 2013 | ods in an [R package] cancertim | |
| 24064420 | c++ | QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. | 2013 | mented in [C++] are avail | |
| 24064416 | python | BioServices: a common Python package to access biological Web Services programmatically. | 2013 | a common [python] package t | |
| 24058058 | python | Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. | 2013 | n c++ and [python] and can b | |
| 24058058 | c++ | Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. | 2013 | ritten in [C++] and pytho | |
| 24058055 | r | customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. | 2013 | prodb: an [R package] to genera | |
| 24045775 | java | Pattern search in BioPAX models. | 2014 | eloped in [java]. source c | |
| 24015679 | r | MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates. | 2013 | ixhmm: an [R package] for chip- | |
| 24013927 | mathlab | Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards. | 2013 | [matlab] code, raw | |
| 24008417 | r | NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. | 2013 | avers: an [R package] for integ | |
| 24006871 | c++ | Pathway-PDT: a flexible pathway analysis tool for nuclear families. | 2013 | mented in [C++] with posi | |
| 23995392 | c++ | PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data. | 2013 | mented in [C++] and suppo | |
| 23995391 | c++ | Consed: a graphical editor for next-generation sequencing. | 2013 | ems or as [C++] source co | |
| 23990418 | r | Multiple alignment-free sequence comparison. | 2013 | ilable as [R package] named 'mu | |
| 23990415 | r | A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure. | 2013 | ovide the [R package] aclust th | |
| 23986565 | r | Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools. | 2013 | kage from [Bioconductor] (http://w | |
| 23981227 | r | NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. | 2013 | asets and [R package] are avail | |
| 23980025 | c++ | MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. | 2013 | mented in [C++] and is av | |
| 23975765 | python | GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. | 2013 | mented in [python] and requi | |
| 23975763 | java | RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. | 2013 | teractive [java] applicati | |
| 23968174 | r | MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. | 2013 | n in perl [and R]. the pipe | |
| 23968174 | perl | MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. | 2013 | ritten in [perl] and r. th | |
| 23966112 | r | Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. | 2013 | ell as an [R package] that impl | |
| 23965047 | r | A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. | 2013 | rt of the [Bioconductor] project a | |
| 23962615 | c++ | fmcsR: mismatch tolerant maximum common substructure searching in R. | 2013 | mented in [C++]. it inclu | |
| 23962615 | r | fmcsR: mismatch tolerant maximum common substructure searching in R. | 2013 | from the [Bioconductor] site (htt | |
| 23962281 | python | Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters. | 2013 | mented in [python], and are | |
| 23958730 | perl | HippDB: a database of readily targeted helical protein-protein interactions. | 2013 | mented in [perl] and suppo | |
| 23958729 | r | iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data. | 2013 | en-source [R package], ibmq. ou | |
| 23958727 | r | Efficient inference of local ancestry. | 2013 | ted as an [R package], which is | |
| 23958726 | r | RDAVIDWebService: a versatile R interface to DAVID. | 2013 | ble as an [R package] from the | |
| 23958724 | r | A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. | 2013 | the gpca [R package] (availabl | |
| 23956305 | r | A Turing test for artificial expression data. | 2013 | d via the [CRAN] package a | |
| 23956303 | c++ | SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. | 2013 | the boost [C++] libraries | |
| 23946504 | java | SubNet: a Java application for subnetwork extraction. | 2013 | subnet: a [java] applicati | |
| 23946503 | python | omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. | 2013 | mented in [python], postgres | |
| 23946501 | python | isomiRID: a framework to identify microRNA isoforms. | 2013 | mand line [python] script av | |
| 23941167 | java | ArkMAP: integrating genomic maps across species and data sources. | 2013 | -updating [java] 'web star | |
| 23937229 | r | RCircos: an R package for Circos 2D track plots. | 2013 | ircos: an [R package] for circo | |
| 23937229 | perl | RCircos: an R package for Circos 2D track plots. | 2013 | rcos is a [perl] language | |
| 23929032 | perl | ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. | 2013 | mented in [perl] as a comp | |
| 23929031 | java | PARSEC: PAtteRn SEarch and Contextualization. | 2013 | mented in [java], javascri | |
| 23929031 | c++ | PARSEC: PAtteRn SEarch and Contextualization. | 2013 | cript and [C++], with all | |
| 23929031 | javascript | PARSEC: PAtteRn SEarch and Contextualization. | 2013 | in java, [javascript] and c++, | |
| 23929030 | java | WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures. | 2013 | requires [java] plugin fo | |
| 23926227 | mathlab | OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes. | 2013 | [matlab] code is a | |
| 23926226 | r | nCal: an R package for non-linear calibration. | 2013 | ncal: an [R package] for non-l | |
| 23918249 | java | The BioPAX Validator. | 2013 | ine tool, [java] library a | |
| 23918247 | java | CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. | 2013 | eloped in [java]. source c | |
| 23900188 | perl | Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. | 2013 | mented in [perl] and suppo | |
| 23885712 | r | DepthTools: an R package for a robust analysis of gene expression data. | 2013 | tools: an [R package] for a rob | |
| 23884480 | python | OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. | 2013 | nted as a [python] script an | |
| 23883280 | r | svapls: an R package to correct for hidden factors of variability in gene expression studies. | 2013 | vapls: an [R package] to correc | |
| 23870110 | java | Mining differential top-k co-expression patterns from time course comparative gene expression datasets. | 2013 | sses. the [java] source co | |
| 23868956 | perl | SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules. | 2013 | mented in [perl], html, cs | |
| 23868956 | javascript | SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules. | 2013 | , css and [javascript] and runni | |
| 23864731 | r | deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis. | 2013 | deltagseg [R package] that perf | |
| 23815292 | c++ | A subgraph isomorphism algorithm and its application to biochemical data. | 2013 | , and our [C++] implement | |
| 23853063 | python | Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. | 2013 | en-source [python] package t | |
| 23846745 | java | SICOP: identifying significant co-interaction patterns. | 2013 | ritten in [java] and accep | |
| 23846743 | python | pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling. | 2013 | pyrmsd: a [python] package f | |
| 23842814 | perl | A new framework for computational protein design through cost function network optimization. | 2013 | (based on [perl] scripts) | |
| 23842812 | r | A genomic random interval model for statistical analysis of genomic lesion data. | 2013 | an [R package] will be f | |
| 23842806 | python | BioSmalltalk: a pure object system and library for bioinformatics. | 2013 | sage than [biopython] and biope | |
| 23842806 | perl | BioSmalltalk: a pure object system and library for bioinformatics. | 2013 | ython and [bioperl] for some | |
| 23837715 | r | TCC: an R package for comparing tag count data with robust normalization strategies. | 2013 | tcc: an [R package] for compa | |
| 23836142 | python | Determining the subcellular location of new proteins from microscope images using local features. | 2013 | ritten in [python] and c++ a | |
| 23836142 | c++ | Determining the subcellular location of new proteins from microscope images using local features. | 2013 | ython and [C++] and is av | |
| 23832245 | java | PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. | 2013 | mented in [java] and avail | |
| 23828785 | java | Rapid similarity search of proteins using alignments of domain arrangements. | 2014 | provide a [java] api for p | |
| 23828782 | c++ | Scalable metagenomic taxonomy classification using a reference genome database. | 2013 | mented in [C++] and is fr | |
| 23825369 | r | mRMRe: an R package for parallelized mRMR ensemble feature selection. | 2013 | mrmre: an [R package] for paral | |
| 23825367 | r | CellMix: a comprehensive toolbox for gene expression deconvolution. | 2013 | llmix, an [R package] that inco | |
| 23821648 | r | Data-based filtering for replicated high-throughput transcriptome sequencing experiments. | 2013 | ed in the [R package] htsfilter | |
| 23818512 | python | BNFinder2: Faster Bayesian network learning and Bayesian classification. | 2013 | mented in [python] and freel | |
| 23812989 | c++ | Predicting protein interactions via parsimonious network history inference. | 2013 | mented in [C++], is open | |
| 23812983 | java | Inference of historical migration rates via haplotype sharing. | 2013 | doris, a [java] implement | |
| 23811095 | java | LNETWORK: an efficient and effective method for constructing phylogenetic networks. | 2013 | uilt as a [java] software | |
| 23803468 | java | Pipit: visualizing functional impacts of structural variations. | 2013 | -platform [java] applicati | |
| 23786769 | r | PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. | 2013 | en-source [R package], ping 2.0 | |
| 23786768 | python | Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. | 2013 | , octave, [python] and c) fo | |
| 23786768 | mathlab | Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. | 2013 | ckage (in [matlab], octave, | |
| 23786315 | python | Bioinformatic pipelines in Python with Leaf. | 2013 | elines in [python] with leaf | |
| 23782613 | java | GPViz: dynamic visualization of genomic regions and variants affecting protein domains. | 2013 | based on [java] 7 and can | |
| 23772051 | r | AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal. | 2013 | ted in an [R package] (http://s | |
| 23766418 | java | Metingear: a development environment for annotating genome-scale metabolic models. | 2013 | mented in [java] with bund | |
| 23766417 | java | UniNovo: a universal tool for de novo peptide sequencing. | 2013 | mented in [java] and teste | |
| 23763826 | java | KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain. | 2013 | ed, using [java] on spring | |
| 23758891 | r | Utilizing protein structure to identify non-random somatic mutations. | 2013 | logy. the [R package] is availa | |
| 23758828 | c | QualComp: a new lossy compressor for quality scores based on rate distortion theory. | 2013 | package, [written in C] and freel | |
| 23758781 | javascript | bioWeb3D: an online webGL 3D data visualisation tool. | 2013 | ritten in [javascript], bioweb3d | |
| 23735186 | python | A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. | 2013 | ritten in [python], and is f | |
| 23735122 | python | Software tool for 3D extraction of germinal centers. | 2013 | ritten in [python] with c ex | |
| 23749961 | java | NOA: a cytoscape plugin for network ontology analysis. | 2013 | n source, [java] program f | |
| 23749960 | javascript | Network2Canvas: network visualization on a canvas with enrichment analysis. | 2013 | with the [javascript] library d | |
| 23749958 | r | PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. | 2013 | ted as an [R package], and sour | |
| 23742985 | perl | Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. | 2013 | forms: a [perl] script (v | |
| 23742983 | python | REDItools: high-throughput RNA editing detection made easy. | 2013 | suite of [python] scripts t | |
| 23740750 | r | Pathview: an R/Bioconductor package for pathway-based data integration and visualization. | 2013 | e through [Bioconductor] and r-for | |
| 23740744 | r | opm: an R package for analysing OmniLog(R) phenotype microarray data. | 2013 | opm: an [R package] for analy | |
| 23740742 | java | WhichCyp: prediction of cytochromes P450 inhibition. | 2013 | whichcyp [java] program a | |
| 23736531 | c++ | NGS++: a library for rapid prototyping of epigenomics software tools. | 2013 | ritten in [C++] using the | |
| 23732275 | javascript | Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. | 2013 | ritten in [javascript] on the cl | |
| 23732273 | c++ | SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles. | 2013 | [C++] source co | |
| 23720490 | r | Drug-target interaction prediction through domain-tuned network-based inference. | 2013 | hrough an [R package] at the fo | |
| 23712657 | c | DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. | 2013 | codes are [written in C] and integ | |
| 23709497 | r | viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. | 2013 | irome: an [R package] for the v | |
| 23709494 | r | Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. | 2013 | [R package] 'triplex' | |
| 23681123 | r | TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. | 2013 | analysis [and R] (http://c | |
| 23677940 | python | Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information. | 2013 | mented in [python] v2.7 and | |
| 23658420 | java | Twine: display and analysis of cis-regulatory modules. | 2013 | wine is a [java] gui with | |
| 23652425 | python | pyGenClean: efficient tool for genetic data clean up before association testing. | 2013 | en source [python] 2.7 softw | |
| 23645815 | java | RegaDB: community-driven data management and analysis for infectious diseases. | 2013 | en in the [java] programmi | |
| 23640718 | mathlab | miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data. | 2013 | [matlab] source co | |
| 23630177 | mathlab | Intervention in gene regulatory networks with maximal phenotype alteration. | 2013 | results, [matlab] source co | |
| 23627667 | r | Steiner tree methods for optimal sub-network identification: an empirical study. | 2013 | nernet on [CRAN] (http://w | |
| 23625999 | c++ | NetworkTrail--a web service for identifying and visualizing deregulated subnetworks. | 2013 | mented in [C++]. networkt | |
| 23620362 | r | RSVSim: an R/Bioconductor package for the simulation of structural variations. | 2013 | ttp://www.[Bioconductor].org. a vi | |
| 23617841 | r | Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution. | 2013 | able from [Bioconductor] (http://w | |
| 23617301 | java | D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements. | 2013 | mented in [java] and provi | |
| 23617269 | mathlab | Ensemble-based prediction of RNA secondary structures. | 2013 | our data, [matlab] software | |
| 23617239 | c++ | An efficient algorithm to perform multiple testing in epistasis screening. | 2013 | mented in [C++] in our ep | |
| 23613487 | python | mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. | 2013 | age/ as a [python] package a | |
| 23595665 | r | CellH5: a format for data exchange in high-content screening. | 2013 | nd at www.[Bioconductor].org/packa | |
| 23595662 | javascript | A self-updating road map of The Cancer Genome Atlas. | 2013 | gine uses [javascript] in conjun | |
| 23595660 | r | Learning gene network structure from time laps cell imaging in RNAi Knock downs. | 2013 | rt of the [Bioconductor] r-package | |
| 23589650 | r | Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. | 2013 | .html and [Bioconductor]. | |
| 23589649 | mathlab | Exome-based analysis for RNA epigenome sequencing data. | 2013 | the [matlab] package ' | |
| 23586463 | javascript | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. | 2013 | using the [javascript] library, | |
| 23577585 | r | Random forest methodology for model-based recursive partitioning: the mobForest package for R. | 2013 | resent an [R package] called m | |
| 23575005 | r | An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS. | 2013 | measures. [R package] and examp | |
| 23574737 | javascript | Biographer: web-based editing and rendering of SBGN compliant biochemical networks. | 2013 | , css and [javascript] and can b | |
| 23574736 | mathlab | OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks. | 2013 | var-boost [matlab] code is a | |
| 23564846 | java | MonaLisa--visualization and analysis of functional modules in biochemical networks. | 2013 | at least [java] 6 and run | |
| 23564843 | python | LibSBMLSim: a reference implementation of fully functional SBML simulator. | 2013 | java, c#, [python] and ruby) | |
| 23564843 | c | LibSBMLSim: a reference implementation of fully functional SBML simulator. | 2013 | ed in the [C programming] language | |
| 23560875 | r | An AUC-based permutation variable importance measure for random forests. | 2013 | ed in the [R package] party for | |
| 23559638 | python | Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. | 2013 | and r and [python] scripts a | |
| 23559638 | r | Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. | 2013 | iled code [and R] and pytho | |
| 23557111 | c++ | CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. | 2013 | n in cuda [C++] and ptx a | |
| 23543414 | r | Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. | 2013 | ed in the [R package] tess, ava | |
| 23539306 | java | FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data. | 2013 | ted using [java] 1.6. it c | |
| 23508970 | mathlab | The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions. | 2013 | port into [matlab]. | |
| 23508967 | mathlab | SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets. | 2013 | en-source [matlab] and gnu o | |
| 23505297 | c++ | TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models. | 2013 | xtensible [C++] implement | |
| 23505296 | python | Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells. | 2013 | complete [python] code is a | |
| 23505295 | c++ | HAL: a hierarchical format for storing and analyzing multiple genome alignments. | 2013 | rehensive [C++] api. a se | |
| 23505294 | mathlab | Identification of cancer fusion drivers using network fusion centrality. | 2013 | [matlab] code impl | |
| 23505292 | java | Brain: biomedical knowledge manipulation. | 2013 | rain is a [java] software | |
| 23493324 | python | ChemoPy: freely available python package for computational biology and chemoinformatics. | 2013 | available [python] package f | |
| 23493321 | perl | Modeling risk stratification in human cancer. | 2013 | tation in [perl], r and ap | |
| 23479353 | java | JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models. | 2013 | df5-based [java] implement | |
| 23476023 | c | Specificity and affinity quantification of protein-protein interactions. | 2013 | mented in [C language], and the | |
| 23471300 | python | freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. | 2013 | equires a [python] interpret | |
| 23471300 | c++ | freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. | 2013 | ter and a [C++] compiler. | |
| 23452827 | perl | BioTile, a Perl based tool for the identification of differentially enriched regions in tiling microarray data. | 2013 | iotile, a [perl] based too | |
| 23452776 | r | virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. | 2013 | bi geo or [Bioconductor]. after es | |
| 23452721 | c++ | MethylPCA: a toolkit to control for confounders in methylome-wide association studies. | 2013 | sks, uses [C++] for cpu a | |
| 23449093 | r | SplicingCompass: differential splicing detection using RNA-seq data. | 2013 | atistical [language r] at http:/ | |
| 23435069 | javascript | BioJS: an open source JavaScript framework for biological data visualization. | 2013 | en source [javascript] framework | |
| 23434837 | mathlab | An improved constraint filtering technique for inferring hidden states and parameters of a biological model. | 2013 | [matlab] code avai | |
| 23428642 | r | DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data. | 2013 | naseq, an [R package] for decon | |
| 23428641 | r | EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. | 2013 | an [R package] containin | |
| 23426256 | python | propy: a tool to generate various modes of Chou's PseAAC. | 2013 | en source [python] package c | |
| 23422340 | mathlab | IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis. | 2013 | en-source [matlab] toolbox f | |
| 23419378 | java | PleioGRiP: genetic risk prediction with pleiotropy. | 2013 | mented in [java], and it i | |
| 23419376 | r | Nozzle: a report generation toolkit for data analysis pipelines. | 2013 | ozzle, an [R package] that prov | |
| 23419375 | r | PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data. | 2013 | ted as an [R package] and avail | |
| 23419374 | java | Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. | 2013 | mented in [java] and is fr | |
| 23418188 | mathlab | Chemical rule-based filtering of MS/MS spectra. | 2013 | the [matlab] source co | |
| 23418185 | python | eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. | 2013 | mework in [python] for rapid | |
| 23413438 | r | Efficient comparison of sets of intervals with NC-lists. | 2013 | , where q [and R] are the s | |
| 23368970 | java | An extensible six-step methodology to automatically generate fuzzy DSSs for diagnostic applications. | 2013 | alized in [java] following | |
| 23396124 | mathlab | Quantifying spatial relationships from whole retinal images. | 2013 | the [matlab] code for | |
| 23396123 | javascript | MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. | 2013 | html and [javascript] with all | |
| 23396118 | r | displayHTS: a R package for displaying data and results from high-throughput screening experiments. | 2013 | layhts: a [R package] for displ | |
| 23394478 | c | Multiple consensus trees: a method to separate divergent genes. | 2013 | us trees, [written in C] was made | |
| 23391497 | python | Coalescent simulation in continuous space. | 2013 | available [python] module. | |
| 23390138 | c++ | Fast thermodynamically constrained flux variability analysis. | 2013 | ritten in [C++] and publi | |
| 23390138 | mathlab | Fast thermodynamically constrained flux variability analysis. | 2013 | exists a [matlab] interface | |
| 23379655 | r | puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis. | 2013 | tion. the [Bioconductor] package p | |
| 23375020 | python | FANTOM: Functional and taxonomic analysis of metagenomes. | 2013 | mented in [python], is platf | |
| 23365410 | python | MosaicFinder: identification of fused gene families in sequence similarity networks. | 2013 | ed in the [python] program f | |
| 23365410 | c++ | MosaicFinder: identification of fused gene families in sequence similarity networks. | 2013 | od in the [C++] program m | |
| 23355290 | c++ | Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. | 2013 | iled into [C++] code that | |
| 23331614 | python | Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data. | 2013 | ted bpms. [python] is the on | |
| 23329415 | java | SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology. | 2013 | ritten in [java] and are p | |
| 23327649 | javascript | Kerfuffle: a web tool for multi-species gene colocalization analysis. | 2013 | mented in [javascript] (using jq | |
| 23324080 | java | JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. | 2013 | file and [java] webstart. | |
| 23323831 | r | GSVA: gene set variation analysis for microarray and RNA-seq data. | 2013 | rt of the [Bioconductor] project a | |
| 23323543 | r | SRAdb: query and use public next-generation sequencing data from within R. | 2013 | sradb [Bioconductor] package p | |
| 23320794 | r | Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups. | 2012 | (umpire) [R package]. we estim | |
| 23314326 | c++ | Reconciling differential gene expression data with molecular interaction networks. | 2013 | [C++] software | |
| 23314324 | python | NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. | 2013 | systems. [python] 2.6+ and | |
| 23314322 | perl | gKaKs: the pipeline for genome-level Ka/Ks calculation. | 2013 | mented in [perl] and is fr | |
| 23314125 | r | CePa: an R package for finding significant pathways weighted by multiple network centralities. | 2013 | cepa: an [R package] for findi | |
| 23303511 | java | Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes. | 2013 | -friendly [java] program f | |
| 23303510 | r | HitWalker: variant prioritization for personalized functional cancer genomics. | 2013 | ble as an [R package] from www. | |
| 23303509 | python | ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. | 2013 | in c and [python]. | |
| 23303508 | python | Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. | 2013 | mented in [python] (v2.6) an | |
| 23303507 | r | SIBER: systematic identification of bimodally expressed genes using RNAseq data. | 2013 | the [R package] siber is | |
| 23282007 | mathlab | CFMDS: CUDA-based fast multidimensional scaling for genome-scale data. | 2012 | ng c# and [matlab]. in our e | |
| 23300135 | perl | MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. | 2013 | en-source [perl] implement | |
| 23292739 | mathlab | KEGGParser: parsing and editing KEGG pathway maps in Matlab. | 2013 | y maps in [matlab]. | |
| 23274212 | r | rBiopaxParser--an R package to parse, modify and visualize BioPAX data. | 2013 | arser--an [R package] to parse, | |
| 25937946 | mathlab | Exploiting identifiability and intergene correlation for improved detection of differential expression. | 2013 | rithms in [matlab] and in r | |
| 23271269 | mathlab | Inference of gene regulatory networks from genome-wide knockout fitness data. | 2013 | [matlab] code and | |
| 23267175 | c++ | Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling. | 2013 | mented in [C++] and avail | |
| 23267174 | r | Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. | 2013 | cellassay [R package] available | |
| 23242262 | java | Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. | 2013 | original [java] implement | |
| 23242262 | python | Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. | 2013 | nd its r, [python] and matla | |
| 23242262 | c++ | Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. | 2013 | ctave and [C++]. the c so | |
| 23242262 | r | Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. | 2013 | g for the [R package] minerva. | |
| 23242262 | mathlab | Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers. | 2013 | ython and [matlab] wrappers. | |
| 23233655 | perl | Characterization of disordered proteins with ENSEMBLE. | 2013 | dded in a [perl] wrapper. | |
| 23220574 | python | Nestly--a framework for running software with nested parameter choices and aggregating results. | 2013 | nestly, a [python] package t | |
| 23216942 | r | A novel approach for biomarker selection and the integration of repeated measures experiments from two assays. | 2012 | ed in the [R package] mixomics | |
| 23216884 | perl | Flexible and efficient genome tiling design with penalized uniqueness score. | 2012 | nted as a [perl] program, | |
| 23202745 | r | BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters. | 2013 | bluesnp: [R package] for highl | |
| 23178637 | java | Bioclipse-R: integrating management and visualization of life science data with statistical analysis. | 2013 | a set of [java] plug-ins | |
| 23178637 | r | Bioclipse-R: integrating management and visualization of life science data with statistical analysis. | 2013 | ogramming [language r]. the syne | |
| 23176119 | r | A tutorial in displaying mass spectrometry-based proteomic data using heat maps. | 2012 | ogramming [language r], which ca | |
| 23175757 | mathlab | An effective framework for reconstructing gene regulatory networks from genetical genomics data. | 2013 | a [matlab] implement | |
| 23172864 | javascript | Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. | 2013 | mented in [javascript] with all | |
| 23172861 | java | DOOSS: a tool for visual analysis of data overlaid on secondary structures. | 2013 | ritten in [java] and is av | |
| 23164367 | c++ | Estimating relative abundances of proteins from shotgun proteomics data. | 2012 | eins. the [C++] source co | |
| 23162084 | java | An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values. | 2013 | mented in [java], mysql, a | |
| 23162059 | java | VAGUE: a graphical user interface for the Velvet assembler. | 2013 | rgets the [java] virtual m | |
| 23162058 | perl | VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. | 2013 | mented in [perl] and is av | |
| 23162057 | c++ | Largenet2: an object-oriented programming library for simulating large adaptive networks. | 2013 | largenet2 [C++] library p | |
| 23151154 | r | Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects. | 2012 | developed [R package] is flexib | |
| 23148484 | c++ | Oculus: faster sequence alignment by streaming read compression. | 2012 | dependent [C++] source co | |
| 23137144 | r | Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. | 2012 | orms. the [R package] ippd impl | |
| 23129301 | java | HD-CNV: hotspot detector for copy number variants. | 2013 | en source [java] code and | |
| 23129297 | r | DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. | 2013 | [R package] (submitte | |
| 23113980 | r | A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies. | 2012 | nking. an [R package] implement | |
| 23110970 | java | 13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis. | 2013 | ard) with [java] and pytho | |
| 23110970 | python | 13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis. | 2013 | java and [python] add-ons t | |
| 23110970 | c++ | 13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis. | 2013 | mented in [C++] (iso/iec | |
| 23109181 | java | ADAM: automated data management for research datasets. | 2013 | ted using [java] and suppo | |
| 23104889 | mathlab | SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. | 2013 | face with [matlab], and seve | |
| 23104886 | c++ | STAR: ultrafast universal RNA-seq aligner. | 2013 | tandalone [C++] code. sta | |
| 23104885 | java | XiP: a computational environment to create, extend and share workflows. | 2013 | oth r and [java], the anal | |
| 23102059 | java | Combing the hairball with BioFabric: a new approach for visualization of large networks. | 2012 | en-source [java] applicati | |
| 23097421 | python | FFPopSim: an efficient forward simulation package for the evolution of large populations. | 2012 | ses and a [python] interface | |
| 23097421 | c++ | FFPopSim: an efficient forward simulation package for the evolution of large populations. | 2012 | ection of [C++] classes a | |
| 23097420 | r | AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data. | 2013 | lable via [Bioconductor] at the ur | |
| 23093610 | c++ | Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. | 2013 | nted in a [C++] program a | |
| 23083219 | r | dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. | 2012 | ovided an [R package] for dspig | |
| 23046475 | perl | Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213. | 2012 | nd custom [perl] scripts i | |
| 23046276 | java | BirdsEyeView (BEV): graphical overviews of experimental data. | 2012 | able as a [java] webstart | |
| 23052038 | perl | Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. | 2012 | ted using [perl] scripts a | |
| 23047557 | c++ | SCALCE: boosting sequence compression algorithms using locally consistent encoding. | 2012 | mented in [C++] with both | |
| 23044551 | c++ | COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. | 2012 | mented in [C++] and is fr | |
| 23044545 | r | fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. | 2012 | rough the [Bioconductor] project. | |
| 23044544 | c++ | KGBassembler: a karyotype-based genome assembler for Brassicaceae species. | 2012 | mented in [C++] with a gr | |
| 23044538 | c++ | MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit. | 2012 | ritten in [C++] and licen | |
| 23043260 | python | Frnakenstein: multiple target inverse RNA folding. | 2012 | nted as a [python] program c | |
| 23031277 | java | VarioML framework for comprehensive variation data representation and exchange. | 2012 | d data. a [java] implement | |
| 23023981 | perl | FeatureStack: Perl module for comparative visualization of gene features. | 2012 | urestack: [perl] module fo | |
| 23020243 | r | QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data. | 2012 | ssible to [Bioconductor]'s computa | |
| 23014632 | c | SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. | 2012 | olpred is [written in C] and is av | |
| 23014630 | r | integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory. | 2012 | the [R package] integirty | |
| 22989518 | java | MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. | 2012 | en-source [java] library j | |
| 22982574 | mathlab | Efficient methods for identifying mutated driver pathways in cancer. | 2012 | a [matlab] package o | |
| 22982573 | java | DLRS: gene tree evolution in light of a species tree. | 2012 | lable for [java] se 6+ und | |
| 22982573 | c++ | DLRS: gene tree evolution in light of a species tree. | 2012 | tly older [C++] version a | |
| 22976081 | c++ | Phylogenetics, likelihood, evolution and complexity. | 2012 | mented in [C++] and suppo | |
| 22976081 | perl | Phylogenetics, likelihood, evolution and complexity. | 2012 | accessory [perl] scripts a | |
| 22974078 | r | Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling). | 2012 | esigns in [Bioconductor] (wavetili | |
| 22962481 | c++ | Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. | 2012 | plemented [C++] and mathe | |
| 22962477 | mathlab | Comprehensive estimation of input signals and dynamics in biochemical reaction networks. | 2012 | [matlab] code is a | |
| 22962475 | python | Random sampling of elementary flux modes in large-scale metabolic networks. | 2012 | tation in [python] is freely | |
| 22962461 | mathlab | Multiple instance learning of Calmodulin binding sites. | 2012 | [matlab] code for | |
| 22962456 | c++ | Evolution of gene neighborhoods within reconciled phylogenies. | 2012 | [C++] implement | |
| 22962455 | mathlab | Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping. | 2012 | mented in [matlab]. source c | |
| 22962454 | java | An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. | 2012 | mented in [java] and r and | |
| 22962454 | r | An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. | 2012 | d in java [and R] and is fr | |
| 22962447 | c++ | Long read alignment based on maximal exact match seeds. | 2012 | ritten in [C++], and all | |
| 22962345 | python | Pythoscape: a framework for generation of large protein similarity networks. | 2012 | mented in [python] for proce | |
| 22962343 | java | ImgLib2--generic image processing in Java. | 2012 | essing in [java]. | |
| 22954632 | python | Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. | 2012 | ool and a [python] library t | |
| 22946927 | r | ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. | 2012 | package, [written in R] and avail | |
| 22945789 | java | JEnsembl: a version-aware Java API to Ensembl data systems. | 2012 | ion-aware [java] api to en | |
| 22945789 | perl | JEnsembl: a version-aware Java API to Ensembl data systems. | 2012 | -specific [perl] apis for | |
| 22942023 | python | CSB: a Python framework for structural bioinformatics. | 2012 | csb: a [python] framework | |
| 22942019 | r | A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. | 2012 | d into an [R package] called ex | |
| 22923307 | r | FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. | 2012 | the [R package] 'facpad' | |
| 22923303 | r | COMPADRE: an R and web resource for pathway activity analysis by component decompositions. | 2012 | adre. the [R package] is also a | |
| 22923296 | c | HiTC: exploration of high-throughput 'C' experiments. | 2012 | hroughput ['C'] experimen | |
| 22923296 | r | HiTC: exploration of high-throughput 'C' experiments. | 2012 | the [R package] hitc is a | |
| 22923295 | c++ | RazerS 3: faster, fully sensitive read mapping. | 2012 | mented in [C++] and openm | |
| 22923294 | java | The GlycomeAtlas tool for visualizing and querying glycome data. | 2012 | site as a [java] applet, i | |
| 22923293 | python | TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes. | 2012 | mand-line [python] toolkit f | |
| 22914219 | mathlab | Intensity quantile estimation and mapping--a novel algorithm for the correction of image non-uniformity bias in HCS data. | 2012 | [matlab] function | |
| 22914218 | java | Qualimap: evaluating next-generation sequencing alignment data. | 2012 | alimap, a [java] applicati | |
| 22909249 | python | Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. | 2012 | e built a [python] software | |
| 22892030 | java | SDAR: a practical tool for graphical analysis of two-dimensional data. | 2012 | ftware in [java] with a us | |
| 22877864 | java | PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. | 2012 | dependent [java] applicati | |
| 22877863 | java | BioJava: an open-source framework for bioinformatics in 2012. | 2012 | ta in the [java] programmi | |
| 22870940 | r | Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. | 2012 | it in an [R package] called cn | |
| 22863767 | mathlab | Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. | 2012 | mented by [matlab] is freely | |
| 22863766 | r | An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection. | 2012 | an [R package] suite for | |
| 22856649 | java | A resource for benchmarking the usefulness of protein structure models. | 2012 | irements: [java] runtime e | |
| 22856649 | perl | A resource for benchmarking the usefulness of protein structure models. | 2012 | ); mysql, [perl] dbi and d | |
| 22856649 | javascript | A resource for benchmarking the usefulness of protein structure models. | 2012 | se); php, [javascript], jmol scr | |
| 22847934 | mathlab | A MATLAB toolbox for structural kinetic modeling. | 2012 | a [matlab] toolbox f | |
| 22847932 | r | easyRNASeq: a bioconductor package for processing RNA-Seq data. | 2012 | aseq', an [R package] that simp | |
| 22846331 | r | Estimation of sequencing error rates in short reads. | 2012 | ted in an [R package], which ca | |
| 22820205 | python | ANGES: reconstructing ANcestral GEnomeS maps. | 2012 | suite of [python] programs | |
| 22820202 | java | SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts. | 2012 | tion is a [java] program t | |
| 22815360 | r | DanteR: an extensible R-based tool for quantitative analysis of -omics data. | 2012 | graphical [R package] that feat | |
| 22815359 | python | Quantifying uniformity of mapped reads. | 2012 | en source [python] script th | |
| 22800377 | c++ | Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. | 2012 | ritten in [C++] and is co | |
| 22796960 | r | GAPIT: genome association and prediction integrated tool. | 2012 | eloped an [R package] called ge | |
| 22796958 | r | A regression model for estimating DNA copy number applied to capture sequencing data. | 2012 | nted in c [and R] and the c | |
| 22796955 | r | MALDIquant: a versatile R package for the analysis of mass spectrometry data. | 2012 | versatile [R package] for the a | |
| 22789589 | r | iBBiG: iterative binary bi-clustering of gene sets. | 2012 | ed in the [Bioconductor] package i | |
| 22788675 | java | A graph-based approach for designing extensible pipelines. | 2012 | n and the [java] executabl | |
| 22782551 | r | Efficient sampling for Bayesian inference of conjunctive Bayesian networks. | 2012 | an [R package] including | |
| 22782546 | java | CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. | 2012 | , c++ and [java]. | |
| 22782546 | c++ | CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. | 2012 | ted in r, [C++] and java. | |
| 22782546 | r | CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. | 2012 | g and via [Bioconductor] version 2 | |
| 22772947 | mathlab | TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies. | 2012 | ilable as [matlab] code or e | |
| 22743227 | perl | PurityEst: estimating purity of human tumor samples using next-generation sequencing data. | 2012 | mented in [perl] and is av | |
| 22743226 | python | RSeQC: quality control of RNA-seq experiments. | 2012 | ritten in [python] and c. so | |
| 22743223 | mathlab | A bioimage informatics approach to automatically extract complex fungal networks. | 2012 | the [matlab] toolbox i | |
| 22734019 | r | Integrating literature-constrained and data-driven inference of signalling networks. | 2012 | ed in the [R package] cnorfeede | |
| 22730434 | python | gSearch: a fast and flexible general search tool for whole-genome sequencing. | 2012 | ruby and [python]. | |
| 22730434 | perl | gSearch: a fast and flexible general search tool for whole-genome sequencing. | 2012 | s such as [perl], ruby and | |
| 22716030 | c++ | EGNAS: an exhaustive DNA sequence design algorithm. | 2012 | ized in a [C++] program. | |
| 22713124 | r | Down-weighting overlapping genes improves gene set analysis. | 2012 | ted as an [R package] available | |
| 22702410 | r | Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling. | 2012 | s2mds: an [R package] for compa | |
| 22698142 | python | Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2. | 2012 | ritten in [python] language | |
| 22694346 | r | Bayesian model to detect phenotype-specific genes for copy number data. | 2012 | eloped an [R package], called b | |
| 22692220 | r | mcaGUI: microbial community analysis R-Graphical User Interface (GUI). | 2012 | ttp://www.[Bioconductor].org/packa | |
| 22689766 | mathlab | Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. | 2012 | mented in [matlab] and are a | |
| 22689388 | r | synbreed: a framework for the analysis of genomic prediction data using R. | 2012 | t a novel [R package] named syn | |
| 22682516 | r | ROCS: a reproducibility index and confidence score for interaction proteomics studies. | 2012 | ble as an [R package] called r | |
| 22676372 | c++ | PollenCALC: software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species. | 2012 | ritten in [C++] programmi | |
| 22668791 | mathlab | Borrowing strength: a likelihood ratio test for related sparse signals. | 2012 | the [matlab] code is a | |
| 22668789 | r | SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components. | 2012 | csa is an [R package] for the a | |
| 22668788 | python | DiNuP: a systematic approach to identify regions of differential nucleosome positioning. | 2012 | mented in [python] and is fr | |
| 22661647 | java | BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. | 2012 | mented in [java] and freel | |
| 22647087 | python | PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. | 2012 | pyms: a [python] toolkit f | |
| 22647057 | r | Detection and correction of probe-level artefacts on microarrays. | 2012 | step. an [R package] is freely | |
| 22645166 | python | An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. | 2012 | mented in [python], mysql, a | |
| 22635606 | java | Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. | 2012 | mented in [java] (v1.6) an | |
| 22635605 | r | BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model. | 2012 | atman--an [R package] for the a | |
| 22624611 | java | TreeSnatcher plus: capturing phylogenetic trees from images. | 2012 | ui-driven [java] applicati | |
| 22607271 | java | Natural product-likeness score revisited: an open-source, open-data implementation. | 2012 | tandalone [java] package f | |
| 22607234 | c++ | Multiple structure alignment with msTALI. | 2012 | ions. the [C++] source co | |
| 22595209 | r | flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding. | 2012 | the [R package] flowpeaks | |
| 22595208 | mathlab | Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. | 2012 | s sampler [matlab] package i | |
| 22595207 | r | R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression. | 2012 | ndziorski [using R], a freely | |
| 22594948 | r | rCUR: an R package for CUR matrix decomposition. | 2012 | rcur: an [R package] for cur m | |
| 22594911 | java | Workflows for microarray data processing in the Kepler environment. | 2012 | thon, and [java] programmi | |
| 22594911 | python | Workflows for microarray data processing in the Kepler environment. | 2012 | in the r, [python], and java | |
| 22592383 | r | Fast computation for genome-wide association studies using boosted one-step statistics. | 2012 | the [R package] 'boss' is | |
| 22591016 | c++ | Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. | 2012 | provide a [C++] implement | |
| 22581181 | r | SRMA: an R package for resequencing array data analysis. | 2012 | srma: an [R package] for reseq | |
| 22581178 | r | iFad: an integrative factor analysis model for drug-pathway association inference. | 2012 | the [R package] 'ifad' an | |
| 22581176 | c++ | Software support for SBGN maps: SBGN-ML and LibSBGN. | 2012 | ilable in [C++] and java) | |
| 22576175 | r | CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. | 2012 | en-source [R package] calmate, | |
| 22568821 | java | PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. | 2012 | dependent [java] software | |
| 22563068 | r | Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data. | 2012 | ed in the [R package] birta, wh | |
| 22563066 | python | Identifying differentially expressed transcripts from RNA-seq data with biological variation. | 2012 | n c++ and [python]. the soft | |
| 22563066 | c++ | Identifying differentially expressed transcripts from RNA-seq data with biological variation. | 2012 | ritten in [C++] and pytho | |
| 22559915 | c++ | EpiFire: An open source C++ library and application for contact network epidemiology. | 2012 | en source [C++] library a | |
| 22559006 | r | Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses. | 2012 | able from [Bioconductor]. | |
| 22536965 | python | CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. | 2012 | ritten in [python], taking a | |
| 22543499 | mathlab | Truncated branch and bound achieves efficient constraint-based genetic design. | 2012 | ted using [matlab] and is fr | |
| 22543367 | java | Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. | 2012 | mented in [java] and suppo | |
| 22543366 | java | DAVID-WS: a stateful web service to facilitate gene/protein list analysis. | 2012 | ritten in [java], perl, py | |
| 22543366 | python | DAVID-WS: a stateful web service to facilitate gene/protein list analysis. | 2012 | va, perl, [python] and matla | |
| 22543366 | perl | DAVID-WS: a stateful web service to facilitate gene/protein list analysis. | 2012 | in java, [perl], python a | |
| 22539671 | python | DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. | 2012 | sy-to-use [python] gui appli | |
| 22539669 | python | Statistical interpretation of machine learning-based feature importance scores for biomarker discovery. | 2012 | [python] source co | |
| 22539669 | mathlab | Statistical interpretation of machine learning-based feature importance scores for biomarker discovery. | 2012 | ll as the [matlab] scripts u | |
| 22539667 | java | CNVRuler: a copy number variation-based case-control association analysis tool. | 2012 | ams r and [java] from sun | |
| 22539666 | perl | PSI-Search: iterative HOE-reduced profile SSEARCH searching. | 2012 | ritten in [perl] for linux | |
| 22531217 | c++ | Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. | 2012 | ritten in [C++], licensed | |
| 22531214 | perl | NuST: analysis of the interplay between nucleoid organization and gene expression. | 2012 | template [perl] code for | |
| 22513995 | r | NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. | 2012 | xtensible [R package] for the p | |
| 22513994 | r | TSSi--an R package for transcription start site identification from 5' mRNA tag data. | 2012 | tssi--an [R package] for trans | |
| 22513993 | c++ | INRICH: interval-based enrichment analysis for genome-wide association studies. | 2012 | tandalone [C++] program, | |
| 22508794 | c++ | pIRS: Profile-based Illumina pair-end reads simulator. | 2012 | ritten in [C++] and perl, | |
| 22508794 | perl | pIRS: Profile-based Illumina pair-end reads simulator. | 2012 | n c++ and [perl], and is f | |
| 22507266 | r | 'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences. | 2012 | friendly [R package], compatib | |
| 22500002 | java | Bpipe: a tool for running and managing bioinformatics pipelines. | 2012 | ring only [java] as a depe | |
| 22500001 | c++ | optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants. | 2012 | mented in [C++] for use o | |
| 22492646 | mathlab | CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. | 2012 | e popular [matlab] computati | |
| 22492641 | r | Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions. | 2012 | able from [CRAN] (www.r-pr | |
| 22492640 | java | PaGeFinder: quantitative identification of spatiotemporal pattern genes. | 2012 | nloadable [java] programs | |
| 22492638 | r | Detection of differentially expressed segments in tiling array data. | 2012 | the [R package] including | |
| 22492314 | java | Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses. | 2012 | mented in [java], supporte | |
| 22492311 | r | Rknots: topological analysis of knotted biopolymers with R. | 2012 | flexible [R package] providing | |
| 22479706 | c++ | Network-based functional enrichment. | 2011 | mented in [C++] and are f | |
| 22467912 | r | Reno: regularized non-parametric analysis of protein lysate array data. | 2012 | ogramming [language r] is availa | |
| 22467906 | c++ | OCAP: an open comprehensive analysis pipeline for iTRAQ. | 2012 | eloped in [C++] and is pr | |
| 22467906 | r | OCAP: an open comprehensive analysis pipeline for iTRAQ. | 2012 | ell as an [R package]. the r pa | |
| 22451269 | r | CpGassoc: an R function for analysis of DNA methylation microarray data. | 2012 | assoc, an [R package] that can | |
| 22426344 | mathlab | Proteus: a web-based, context-specific modelling tool for molecular networks. | 2012 | anguage), [matlab] or fortra | |
| 22426344 | fortran | Proteus: a web-based, context-specific modelling tool for molecular networks. | 2012 | matlab or [fortran] format an | |
| 22419785 | c++ | SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer. | 2012 | mented in [C++] for linux | |
| 22419783 | java | Harmonization of gene/protein annotations: towards a gold standard MEDLINE. | 2012 | mented in [java] and its r | |
| 22402612 | r | rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. | 2012 | rehh: an [R package] to detect | |
| 22390939 | mathlab | Combining multiple approaches for gene microarray classification. | 2012 | the [mathlab] code of t | |
| 22373214 | r | Building gene expression profile classifiers with a simple and efficient rejection option in R. | 2011 | ed in the [R language] and envir | |
| 22383736 | r | Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. | 2012 | e through [Bioconductor]. addition | |
| 22378710 | mathlab | StochSens--Matlab package for sensitivity analysis of stochastic chemical systems. | 2012 | present a [matlab] package, | |
| 22373787 | c++ | Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. | 2012 | the [C++] source co | |
| 22368255 | python | High-quality sequence clustering guided by network topology and multiple alignment likelihood. | 2012 | the [python] software | |
| 22368254 | java | SED-ED, a workflow editor for computational biology experiments written in SED-ML. | 2012 | tandalone [java] applicati | |
| 22368248 | c++ | Unipro UGENE: a unified bioinformatics toolkit. | 2012 | ritten in [C++] using the | |
| 22368246 | r | R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment. | 2012 | able from [CRAN].r-project | |
| 22368246 | mathlab | R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment. | 2012 | relied on [matlab], which is | |
| 22345622 | mathlab | Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq. | 2012 | e/lpchp a [matlab] implement | |
| 22345619 | r | GMD: measuring the distance between histograms with applications on high-throughput sequencing reads. | 2012 | ns) is an [R package] to assess | |
| 22333245 | r | A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. | 2012 | sults and [R package] are avail | |
| 22332239 | java | SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments. | 2012 | mented in [java] to provid | |
| 22330431 | r | ICGE: an R package for detecting relevant clusters and atypical units in gene expression. | 2012 | icge: an [R package] for detec | |
| 22321652 | r | Identification of polymorphic inversions from genotypes. | 2012 | a unified [R package] inversion | |
| 22308148 | javascript | Improving your target-template alignment with MODalign. | 2012 | html and [javascript] with all | |
| 22305354 | r | Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. | 2012 | ed in the [R package] mixomics | |
| 22302572 | python | pymzML--Python module for high-throughput bioinformatics on mass spectrometry data. | 2012 | ension to [python] that offe | |
| 22302569 | java | ArchTEx: accurate extraction and visualization of next-generation sequence data. | 2012 | requires [java] 1.6 or ne | |
| 22302568 | java | Hadoop-BAM: directly manipulating next generation sequencing data in the cloud. | 2012 | icard sam [jdk], so tools | |
| 22292714 | r | graphite - a Bioconductor package to convert pathway topology to gene network. | 2012 | phite - a [Bioconductor] package t | |
| 22285827 | perl | Chado controller: advanced annotation management with a community annotation system. | 2012 | resql and [perl]. | |
| 22262673 | python | medpie: an information extraction package for medical message board posts. | 2012 | [python] 2.6 or 2. | |
| 22253290 | r | IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. | 2012 | ima: an [R package] for high- | |
| 22253280 | java | BamView: visualizing and interpretation of next-generation sequencing read alignments. | 2013 | irements: [java] 1.6 or hi | |
| 22247280 | c++ | Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. | 2012 | en-source [C++] library s | |
| 22247279 | r | Robust rank aggregation for gene list integration and meta-analysis. | 2012 | as a gnu [R package] robustran | |
| 22244131 | python | PyElph - a software tool for gel images analysis and phylogenetics. | 2012 | mented in [python] which is | |
| 22244038 | r | MIPHENO: data normalization for high throughput metabolite analysis. | 2012 | hrough an [R package] in cran. | |
| 22238272 | c++ | A scalable and portable framework for massively parallel variable selection in genetic association studies. | 2012 | mented in [C++] and openc | |
| 22238261 | python | SSuMMo: rapid analysis, comparison and visualization of microbial communities. | 2012 | en source [python] software, | |
| 22238260 | perl | PHACTS, a computational approach to classifying the lifestyle of phages. | 2012 | ed in the [perl] programmi | |
| 22219204 | perl | NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. | 2012 | tool and [perl] module fo | |
| 22210868 | java | VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. | 2012 | ritten in [java], and is f | |
| 22208906 | r | Partition decoupling for multi-gene analysis of gene expression profiling data. | 2011 | sease. an [R package] to carry | |
| 25969751 | perl | Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification. | 2012 | elamp, a [perl] script, w | |
| 22199382 | c++ | Modeling mechanistic biological networks: an advanced Boolean approach. | 2012 | a sample [C++] implement | |
| 22199381 | r | htSeqTools: high-throughput sequencing quality control, processing and visualization in R. | 2012 | provide a [Bioconductor] package w | |
| 22199380 | r | Probe mapping across multiple microarray platforms. | 2012 | pi and an [R package] to map da | |
| 22195644 | r | Structural measures for network biology using QuACN. | 2011 | the [R package] quacn is | |
| 22151882 | c++ | STELLAR: fast and exact local alignments. | 2011 | the seqan [C++] library v | |
| 22177264 | r | GC-content normalization for RNA-Seq data. | 2011 | conductor [R package] edaseq. | |
| 22171336 | mathlab | MTBindingSim: simulate protein binding to microtubules. | 2012 | mented in [matlab] and runs | |
| 22171334 | bash | Detection of microRNAs in color space. | 2012 | a [bash] shell scr | |
| 22171333 | java | JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. | 2012 | ritten in [java]. it is fr | |
| 22171331 | r | Identifying small interfering RNA loci from high-throughput sequencing data. | 2012 | le as the [Bioconductor] (www.bioc | |
| 22171329 | c++ | Transformations for the compression of FASTQ quality scores of next-generation sequencing data. | 2012 | our [C++] implement | |
| 22156367 | r | Optimized application of penalized regression methods to diverse genomic data. | 2011 | he pensim [R package], availabl | |
| 22155946 | r | GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data. | 2012 | olbox: an [R package] for fast | |
| 22155870 | c++ | Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. | 2012 | [C++] source co | |
| 22155869 | perl | Identification and removal of ribosomal RNA sequences from metatranscriptomes. | 2012 | mented in [perl] and can b | |
| 22155866 | r | InFiRe -- a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. | 2012 | ogramming [language r]. for the | |
| 22155862 | java | Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. | 2012 | mented in [java]. it can b | |
| 22151536 | r | Empirical comparison of cross-platform normalization methods for gene expression data. | 2011 | rovide an [R package], conor, c | |
| 22136743 | r | From hybridization theory to microarray data analysis: performance evaluation. | 2011 | able from [Bioconductor], which re | |
| 22135419 | java | DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments. | 2012 | dman: a [java] tool for | |
| 22130594 | perl | PGAP: pan-genomes analysis pipeline. | 2012 | oped with [perl] script on | |
| 22121159 | r | Modelling time course gene expression data with finite mixtures of linear additive models. | 2012 | on of the [R package] flexmix i | |
| 22121158 | c++ | Inferring sequence regions under functional divergence in duplicate genes. | 2012 | rgence. a [C++] program, | |
| 22121157 | mathlab | CellAnimation: an open source MATLAB framework for microscopy assays. | 2012 | en source [matlab] framework | |
| 22115179 | r | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. | 2011 | irefr: an [R package] to manipu | |
| 22113085 | r | MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. | 2012 | ed by the [Bioconductor] project. | |
| 22113083 | java | A novel and versatile computational tool to model translation. | 2012 | ritten in [java], and is h | |
| 22113082 | c++ | GenomicTools: a computational platform for developing high-throughput analytics in genomics. | 2012 | ols and a [C++] api, for | |
| 22110245 | java | PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. | 2012 | spider, a [java] program t | |
| 22110244 | mathlab | FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number. | 2012 | mented in [matlab] r2010b an | |
| 22088846 | java | QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. | 2012 | mented in [java]. it is di | |
| 22088841 | mathlab | NoRSE: noise reduction and state evaluator for high-frequency single event traces. | 2012 | -file for [matlab]. | |
| 22087737 | r | ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. | 2011 | est files [and R] source co | |
| 22085701 | mathlab | A flexible framework for sparse simultaneous component based data integration. | 2011 | ontains a [matlab] implement | |
| 22084255 | java | PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. | 2012 | . it is a [java] servlet t | |
| 22078312 | java | Exact score distribution computation for ontological similarity searches. | 2011 | mented in [java], supports | |
| 22072386 | java | Wavelet-based image fusion in multi-view three-dimensional microscopy. | 2012 | eloped in [java]. the soft | |
| 22072386 | mathlab | Wavelet-based image fusion in multi-view three-dimensional microscopy. | 2012 | mented in [matlab] (the math | |
| 22072385 | python | MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. | 2012 | ble and a [python] script th | |
| 22072385 | c++ | MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. | 2012 | x!tandem [C++] executabl | |
| 22070167 | perl | ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. | 2011 | en source [perl] artistic | |
| 22059886 | c++ | A parallel method for enumerating amino acid compositions and masses of all theoretical peptides. | 2011 | ft visual [C++] and the m | |
| 22057162 | r | A robust clustering algorithm for identifying problematic samples in genome-wide association studies. | 2012 | orithm is [written in R] and is fr | |
| 22057161 | r | Detecting differential binding of transcription factors with ChIP-seq. | 2012 | [R package] dbchip is | |
| 22039209 | r | Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. | 2012 | an [R package], called c | |
| 22039206 | c++ | RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. | 2012 | mented in [C++], the sour | |
| 22034839 | r | Stepwise classification of cancer samples using clinical and molecular data. | 2011 | le at the [Bioconductor] website. | |
| 22034520 | java | SVGMap: configurable image browser for experimental data. | 2012 | svgmap, a [java] applicati | |
| 22034520 | javascript | SVGMap: configurable image browser for experimental data. | 2012 | wser with [javascript] enabled. | |
| 22032770 | java | Improving ontologies by automatic reasoning and evaluation of logical definitions. | 2011 | ovide the [java] software | |
| 22032230 | python | Automated NMR relaxation dispersion data analysis using NESSY. | 2011 | ritten in [python] for multi | |
| 22025481 | perl | Graph accordance of next-generation sequence assemblies. | 2012 | ted in oo [perl] and is av | |
| 22025480 | r | PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). | 2011 | d in perl [and R]. it is fr | |
| 22025480 | perl | PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). | 2011 | mented in [perl] and r. it | |
| 21989326 | java | A hidden Markov model for copy number variant prediction from whole genome resequencing data. | 2011 | mented in [java], zinfande | |
| 22016409 | javascript | VizPrimer: a web server for visualized PCR primer design based on known gene structure. | 2011 | cture and [javascript] to intera | |
| 22016407 | java | PRINCIPLE: a tool for associating genes with diseases via network propagation. | 2011 | iple is a [java] applicati | |
| 22014236 | r | An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. | 2011 | ted as an [R package] called s | |
| 22006916 | python | Enrich: software for analysis of protein function by enrichment and depletion of variants. | 2011 | mented in [python] and is av | |
| 21999355 | r | Comparison of lists of genes based on functional profiles. | 2011 | able from [Bioconductor], http://b | |
| 21995452 | r | Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. | 2011 | rt of the [R package] 'bhc' (ve | |
| 21984758 | mathlab | Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. | 2011 | thod in a [matlab] toolbox c | |
| 21961884 | javascript | Interactive metagenomic visualization in a Web browser. | 2011 | html5 and [javascript] implement | |
| 21955789 | r | Mulcom: a multiple comparison statistical test for microarray data in Bioconductor. | 2011 | y data in [Bioconductor]. | |
| 21949271 | python | Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. | 2011 | flexible [python] library f | |
| 21937664 | r | inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. | 2011 | ds on the [Bioconductor] project's | |
| 21923903 | r | Thawing Frozen Robust Multi-array Analysis (fRMA). | 2011 | resent an [R package], frmatool | |
| 21914187 | mathlab | MetaboLab--advanced NMR data processing and analysis for metabolomics. | 2011 | abolab, a [matlab] based sof | |
| 21908865 | r | Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations. | 2012 | eproduced [using R] code avai | |
| 21873638 | mathlab | Feature-based 3D motif filtering for ribosomal RNA. | 2011 | [matlab] code can | |
| 21865301 | perl | SDRS--an algorithm for analyzing large-scale dose-response data. | 2011 | able from [CPAN] (www.cpan | |
| 21851628 | python | DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. | 2011 | ructures. [python] implement | |
| 21851598 | r | Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. | 2011 | ble as an [R package] timeshift | |
| 21846738 | r | Identifying associations between amino acid changes and meta information in alignments. | 2011 | le on the [CRAN] network a | |
| 21846735 | python | Reconstructing the architecture of the ancestral amniote genome. | 2011 | n c++ and [python], is avail | |
| 21846735 | c++ | Reconstructing the architecture of the ancestral amniote genome. | 2011 | code, in [C++] and pytho | |
| 21840874 | c++ | Conserved and differential gene interactions in dynamical biological systems. | 2011 | e code in [C++] and r is | |
| 21840874 | r | Conserved and differential gene interactions in dynamical biological systems. | 2011 | de in c++ [and R] is availa | |
| 21838867 | r | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches. | 2011 | qmnmr, an [R package] that inte | |
| 21831268 | c++ | Efficient counting of k-mers in DNA sequences using a bloom filter. | 2011 | ritten in [C++] and is gp | |
| 21828086 | r | Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. | 2011 | [CRAN] package ' | |
| 21813478 | c++ | GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion. | 2011 | atlab and [C++], is avail | |
| 21813478 | mathlab | GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion. | 2011 | mented in [matlab] and c++, | |
| 21813477 | java | The GNAT library for local and remote gene mention normalization. | 2011 | the gnat [java] library f | |
| 21813013 | java | RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences. | 2011 | teractive [java] applicati | |
| 21810900 | r | A powerful and flexible approach to the analysis of RNA sequence count data. | 2011 | an [R package] containin | |
| 21804112 | r | Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. | 2011 | compliant [R package] dance is | |
| 21803803 | java | JMassBalance: mass-balanced randomization and analysis of metabolic networks. | 2011 | mented in [java] and freel | |
| 21788211 | perl | RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. | 2011 | the [perl] implement | |
| 21785131 | mathlab | CAM-CM: a signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues. | 2011 | the [matlab] source co | |
| 21784795 | r | Estimating classification probabilities in high-dimensional diagnostic studies. | 2011 | urce code [written in R] is freely | |
| 21784792 | mathlab | GenSSI: a software toolbox for structural identifiability analysis of biological models. | 2011 | e popular [matlab] environme | |
| 21775307 | java | Simple high-throughput annotation pipeline (SHAP). | 2011 | mented in [java], shap rec | |
| 21775306 | java | GaggleBridge: collaborative data analysis. | 2011 | ed in the [java] language | |
| 21775304 | python | Making whole genome multiple alignments usable for biologists. | 2011 | mented in [python] and has b | |
| 21771315 | r | Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. | 2011 | forge and [CRAN] http://dd | |
| 21767381 | perl | Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. | 2011 | ogwalk--a [perl] module to | |
| 21765096 | python | Stage prediction of embryonic stem cell differentiation from genome-wide expression data. | 2011 | e form of [python] scripts a | |
| 21757464 | java | PDBpaint, a visualization webservice to tag protein structures with sequence annotations. | 2011 | the jmol [java] viewer). | |
| 21757464 | perl | PDBpaint, a visualization webservice to tag protein structures with sequence annotations. | 2011 | mented in [perl], with all | |
| 21757463 | c++ | Sufficient statistics and expectation maximization algorithms in phylogenetic tree models. | 2011 | the [C++] source co | |
| 21752800 | mathlab | A novel signal processing approach for the detection of copy number variations in the human genome. | 2011 | tensky/ a [matlab] code for | |
| 21742635 | c++ | DivBayes and SubT: exploring species diversification using Bayesian statistics. | 2011 | leased as [C++] source co | |
| 21742634 | r | PREDA: an R-package to identify regional variations in genomic data. | 2011 | ysis), an [R package] for detec | |
| 21737438 | mathlab | Simulating systems genetics data with SysGenSIM. | 2011 | ncoded in [matlab], and a us | |
| 21737437 | r | APCluster: an R package for affinity propagation clustering. | 2011 | uster: an [R package] for affin | |
| 21727140 | python | ModeRNA server: an online tool for modeling RNA 3D structures. | 2011 | using the [python] language | |
| 21724594 | python | MethylCoder: software pipeline for bisulfite-treated sequences. | 2011 | es only a [python] interpret | |
| 21714896 | r | DOSim: an R package for similarity between diseases based on Disease Ontology. | 2011 | dosim: an [R package] for simil | |
| 21712251 | c++ | Paired-end RAD-seq for de novo assembly and marker design without available reference. | 2011 | perl and [C++] implement | |
| 21712251 | perl | Paired-end RAD-seq for de novo assembly and marker design without available reference. | 2011 | a [perl] and c++ i | |
| 21712248 | java | BRISK--research-oriented storage kit for biology-related data. | 2011 | entation, [java] source co | |
| 21697129 | java | JSBML: a flexible Java library for working with SBML. | 2011 | flexible [java] library f | |
| 21697128 | r | Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. | 2011 | metab: an [R package] for high- | |
| 21697127 | r | A procedure to statistically evaluate agreement of differential expression for cross-species genomics. | 2011 | an [R package] is curren | |
| 21697126 | r | ontoCAT: an R package for ontology traversal and search. | 2011 | tocat: an [R package] for ontol | |
| 21697125 | java | GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. | 2011 | with its [java] source co | |
| 21693065 | r | Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. | 2011 | le in the [R package] mixomics, | |
| 21693013 | r | Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. | 2011 | able in a [Bioconductor] package ' | |
| 21689434 | java | PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. | 2011 | mented in [java], and the | |
| 21685105 | r | vipR: variant identification in pooled DNA using R. | 2011 | ooled dna [using R]. | |
| 21685095 | java | Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. | 2011 | [java] code is a | |
| 21685094 | r | From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. | 2011 | d into an [R package] and tied | |
| 21685091 | mathlab | ccSVM: correcting Support Vector Machines for confounding factors in biological data classification. | 2011 | tation in [matlab] is availa | |
| 21685088 | c++ | StructHDP: automatic inference of number of clusters and population structure from admixed genotype data. | 2011 | ritten in [C++]. the code | |
| 21685086 | python | An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data. | 2011 | mented in [python] 2.7 progr | |
| 21685084 | java | A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. | 2011 | cell. the [java] implement | |
| 21685055 | r | Menu-driven cloud computing and resource sharing for R and Bioconductor. | 2011 | ring data [and R] scripts w | |
| 21685053 | python | CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. | 2011 | source in [python] and c++. | |
| 21685053 | c++ | CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. | 2011 | ython and [C++]. requires | |
| 21685051 | python | Methyl-Analyzer--whole genome DNA methylation profiling. | 2011 | yzer is a [python] package t | |
| 21685046 | r | Noise reduction in genome-wide perturbation screens using linear mixed-effect models. | 2011 | .org. the [R package] htsmix is | |
| 21682923 | r | MLPAstats: an R GUI package for the integrated analysis of copy number alterations using MLPA data. | 2011 | stats, an [R package] designed | |
| 21666268 | java | MGV: a generic graph viewer for comparative omics data. | 2011 | mented in [java] and freel | |
| 21666267 | java | Xwalk: computing and visualizing distances in cross-linking experiments. | 2011 | and-alone [java] applicati | |
| 21666266 | r | Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. | 2011 | en-source [R package] named psc | |
| 21666252 | java | Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. | 2011 | tions for [biojava], bioperl, | |
| 21666252 | python | Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. | 2011 | perl, and [biopython]. orthoxml | |
| 21666252 | perl | Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. | 2011 | biojava, [bioperl], and biop | |
| 21659319 | r | mapDamage: testing for damage patterns in ancient DNA sequences. | 2011 | ols suite [and R] environme | |
| 21659319 | perl | mapDamage: testing for damage patterns in ancient DNA sequences. | 2011 | mage is a [perl] script th | |
| 21653523 | java | The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. | 2011 | mented in [java] and suppo | |
| 21653522 | perl | The variant call format and VCFtools. | 2011 | a general [perl] api. | |
| 21636591 | java | PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). | 2011 | tions and [java] source co | |
| 21622663 | perl | Computational discovery of human coding and non-coding transcripts with conserved splice sites. | 2011 | er with a [perl] implement | |
| 21619703 | java | OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. | 2011 | ration in [java], r and re | |
| 21619662 | c++ | miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM. | 2011 | ritten in [C++], is freel | |
| 21615972 | c++ | MixtureTree: a program for constructing phylogeny. | 2011 | ritten in [C++] is a linu | |
| 21615941 | mathlab | Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. | 2011 | mented in [matlab] had simil | |
| 21615941 | fortran | Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. | 2011 | mented in [fortran], and that | |
| 21612622 | r | rnaSeqMap: a Bioconductor package for RNA sequencing data exploration. | 2011 | seqmap: a [Bioconductor] package f | |
| 21599881 | c++ | TreeRipper web application: towards a fully automated optical tree recognition software. | 2011 | mand line [C++] program f | |
| 21596792 | c++ | linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. | 2011 | ritten in [C++] and desig | |
| 21596792 | r | linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. | 2011 | kcomm: an [R package] for the g | |
| 21596789 | java | GenPlay, a multipurpose genome analyzer and browser. | 2011 | ritten in [java] and runs | |
| 21595965 | javascript | Web-based metabolic network visualization with a zooming user interface. | 2011 | ritten in [javascript] for the c | |
| 21595880 | r | Genotype calling in tetraploid species from bi-allelic marker data using mixture models. | 2011 | ed in the [R package] fittetra, | |
| 21593133 | mathlab | An ensemble biclustering approach for querying gene expression compendia with experimental lists. | 2011 | compiled [matlab] code is a | |
| 21593132 | java | Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. | 2011 | [java] bioinform | |
| 21586520 | java | Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management. | 2011 | mented in [java], apache-d | |
| 21586517 | perl | Hidden conformations in protein structures. | 2011 | a [perl] script im | |
| 21561920 | r | Model-based gene set analysis for Bioconductor. | 2011 | rs of the [R language]. our pack | |
| 21554689 | r | Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data. | 2011 | available [R package] 'penalize | |
| 21551149 | c++ | An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences. | 2011 | e related [C++] source co | |
| 21551147 | mathlab | The role of indirect connections in gene networks in predicting function. | 2011 | ovided in [matlab] m-code. | |
| 21551146 | c++ | Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. | 2011 | ten in c, [C++] and perl | |
| 21551146 | c | Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. | 2011 | leaff are [written in C], c++ and | |
| 21551146 | perl | Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. | 2011 | , c++ and [perl] for linux | |
| 21551143 | c++ | A multiple network learning approach to capture system-wide condition-specific responses. | 2011 | [C++] code can | |
| 21551136 | python | BINOCh: binding inference from nucleosome occupancy changes. | 2011 | en source [python] package i | |
| 21548938 | r | ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs. | 2011 | ilable in [Bioconductor]. | |
| 21546399 | r | Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles. | 2011 | ality: an [R package] for testi | |
| 21546396 | java | famCNV: copy number variant association for quantitative traits in families. | 2011 | the [java] package i | |
| 21546394 | java | ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms. | 2011 | mented in [java] 1.6 and s | |
| 21546390 | mathlab | Multiple-rule bias in the comparison of classification rules. | 2011 | mented in [matlab]. the sour | |
| 21535899 | perl | An automated homology-based approach for identifying transposable elements. | 2011 | numerous [bioperl] scripts. | |
| 21535878 | java | SNPPicker: high quality tag SNP selection across multiple populations. | 2011 | scripts, [java] source co | |
| 21535878 | perl | SNPPicker: high quality tag SNP selection across multiple populations. | 2011 | runtime. [perl] scripts, | |
| 21531770 | r | parmigene--a parallel R package for mutual information estimation and gene network reconstruction. | 2011 | parallel [R package] for mutua | |
| 21531769 | c++ | A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. | 2011 | the [C++] source co | |
| 21527044 | r | Sequential interim analyses of survival data in DNA microarray experiments. | 2011 | as a new [R package] 'survgene | |
| 21527030 | python | STSE: Spatio-Temporal Simulation Environment Dedicated to Biology. | 2011 | org/. the [python] source co | |
| 21521499 | python | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. | 2011 | d in c++, [python], and perl | |
| 21521499 | c++ | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. | 2011 | mented in [C++], python, | |
| 21521499 | perl | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. | 2011 | thon, and [perl] and has b | |
| 21513508 | java | The proteogenomic mapping tool. | 2011 | ncludes a [java] implement | |
| 21511716 | java | Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models. | 2011 | en-source [java] library j | |
| 21511714 | java | CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling. | 2011 | en-source [java] applicati | |
| 21489225 | c++ | Processing SPARQL queries with regular expressions in RDF databases. | 2011 | mework in [C++] and condu | |
| 21505037 | python | A graphical interface for the FoldX forcefield. | 2011 | ritten in [python] and is fr | |
| 21505033 | c++ | Rgtsp: a generalized top scoring pairs package for class prediction. | 2011 | full [C++] source co | |
| 21505033 | r | Rgtsp: a generalized top scoring pairs package for class prediction. | 2011 | code and [R package] rgtsp are | |
| 21504561 | r | PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. | 2011 | volution, [written in R], using th | |
| 21501497 | java | Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars. | 2011 | table and [java] source co | |
| 21501495 | python | Screening synteny blocks in pairwise genome comparisons through integer programming. | 2011 | izations. [python] codes and | |
| 21501472 | r | SAQC: SNP array quality control. | 2011 | ftware is [written in R] and r-gui | |
| 21498550 | r | Exon array data analysis using Affymetrix power tools and R statistical software. | 2011 | wer tools [and R] statistic | |
| 21498403 | perl | PathScan: a tool for discerning mutational significance in groups of putative cancer genes. | 2011 | mented in [perl] and is av | |
| 21498400 | java | BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. | 2011 | en-source [java] applicati | |
| 21498399 | r | Normalizing bead-based microRNA expression data: a measurement error model-based approach. | 2011 | asets and [R package] are avail | |
| 21498398 | r | OTUbase: an R infrastructure package for operational taxonomic unit data. | 2011 | ase is an [R package] designed | |
| 21496265 | java | SNP-based pathway enrichment analysis for genome-wide association studies. | 2011 | thod in a [java] software | |
| 21493657 | java | 'Sciencenet'--towards a global search and share engine for all scientific knowledge. | 2011 | based on [java] 1.6. | |
| 21493657 | python | 'Sciencenet'--towards a global search and share engine for all scientific knowledge. | 2011 | ritten in [python] 2.7, and | |
| 21493652 | c++ | BamTools: a C++ API and toolkit for analyzing and managing BAM files. | 2011 | mtools: a [C++] api and t | |
| 21486937 | java | Cobweb: a Java applet for network exploration and visualisation. | 2011 | cobweb: a [java] applet fo | |
| 21478488 | python | Reliability-oriented bioinformatic networks visualization. | 2011 | n c++ and [python], and cons | |
| 21478488 | c++ | Reliability-oriented bioinformatic networks visualization. | 2011 | ritten in [C++] and pytho | |
| 21478487 | c++ | Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. | 2011 | a [C++] and perl | |
| 21478487 | perl | Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. | 2011 | a c++ and [perl] implement | |
| 21471018 | r | Multi-platform segmentation for joint detection of copy number variants. | 2011 | ted in an [R package] mpss, and | |
| 21471012 | python | ProDy: protein dynamics inferred from theory and experiments. | 2011 | veloped a [python] package, | |
| 21471010 | r | Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. | 2011 | from www.[CRAN].r-project | |
| 21450717 | r | A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. | 2011 | e via the [Bioconductor] repositor | |
| 21450711 | r | pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. | 2011 | ge on the [CRAN] repositor | |
| 21447171 | c++ | DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. | 2011 | n in cuda [C++] and mpi. | |
| 21422072 | r | anota: Analysis of differential translation in genome-wide studies. | 2011 | the anota [Bioconductor] package, | |
| 21414990 | r | AStream: an R package for annotating LC/MS metabolomic data. | 2011 | tream: an [R package] for annot | |
| 21414234 | java | ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. | 2011 | ension of [java] algorithm | |
| 21414208 | r | pROC: an open-source package for R and S+ to analyze and compare ROC curves. | 2011 | rough the [CRAN] and csan | |
| 21398675 | c++ | fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. | 2011 | coal is a [C++] program c | |
| 21398674 | r | TEQC: an R package for quality control in target capture experiments. | 2011 | teqc: an [R package] for quali | |
| 21398673 | r | PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies. | 2011 | the perl [and R] scripts a | |
| 21398673 | perl | PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies. | 2011 | the [perl] and r scr | |
| 21398670 | r | Identification and quantification of metabolites in (1)H NMR spectra by Bayesian model selection. | 2011 | the [R package] bquant is | |
| 21398667 | c++ | GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. | 2011 | geco++: a [C++] library f | |
| 21388547 | c++ | The dChip survival analysis module for microarray data. | 2011 | in visual [C++] also enab | |
| 21385435 | java | compomics-utilities: an open-source Java library for computational proteomics. | 2011 | en-source [java] library f | |
| 21372081 | mathlab | Mixtures of common t-factor analyzers for clustering high-dimensional microarray data. | 2011 | mented in [matlab]. the matl | |
| 21342585 | c++ | Repeat-aware modeling and correction of short read errors. | 2011 | mented in [C++] and is fr | |
| 21342575 | python | HDX-analyzer: a novel package for statistical analysis of protein structure dynamics. | 2011 | using r, [python], and rpy2 | |
| 21342575 | r | HDX-analyzer: a novel package for statistical analysis of protein structure dynamics. | 2011 | etry data [using R], python, | |
| 21367873 | r | SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data. | 2011 | jamda: an [R package] to predic | |
| 21367872 | java | Human variation database: an open-source database template for genomic discovery. | 2011 | -platform [java] api is pr | |
| 21357575 | mathlab | STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB. | 2011 | box 2 for [matlab]. | |
| 21357574 | r | aCGH.Spline--an R package for aCGH dye bias normalization. | 2011 | pline--an [R package] for acgh | |
| 21352572 | perl | BIO::Phylo-phyloinformatic analysis using perl. | 2011 | sis using [perl]. | |
| 21352538 | python | A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines. | 2011 | elines in [python] ('papy'). | |
| 21349873 | java | AGRA: analysis of gene ranking algorithms. | 2011 | mented in [java] and runni | |
| 21349869 | r | R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data. | 2011 | ttp://www.[Bioconductor].org/. a v | |
| 21349867 | java | Interactive, multiscale navigation of large and complicated biological networks. | 2011 | [java] implement | |
| 21335612 | c++ | fconv: Format conversion, manipulation and feature computation of molecular data. | 2011 | license. [C++] sources a | |
| 21330291 | c++ | libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. | 2011 | libfbi: a [C++] implement | |
| 21330289 | r | Defining an informativeness metric for clustering gene expression data. | 2011 | conductor [R package] attract; | |
| 21330288 | python | Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. | 2011 | a c++ and [python] implement | |
| 21330288 | c++ | Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. | 2011 | a [C++] and pytho | |
| 21325302 | python | Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows. | 2011 | in ruby, [python] and php. | |
| 21317143 | r | Cross-platform comparison of microarray data using order restricted inference. | 2011 | nted in c [and R] is availa | |
| 21310747 | c++ | Entropy-accelerated exact clustering of protein decoys. | 2011 | our [C++] software | |
| 21310746 | mathlab | FISH Finder: a high-throughput tool for analyzing FISH images. | 2011 | tandalone [matlab] applicati | |
| 21300702 | r | tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor. | 2011 | ssion for [Bioconductor]. | |
| 21300701 | c++ | HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes. | 2011 | mented in [C++] and perl, | |
| 21300701 | perl | HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes. | 2011 | n c++ and [perl], is avail | |
| 21296754 | c++ | SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent. | 2011 | eloped in [C++] and can b | |
| 21296752 | java | DDN: a caBIG® analytical tool for differential network analysis. | 2011 | tandalone [java] applicati | |
| 21296752 | mathlab | DDN: a caBIG® analytical tool for differential network analysis. | 2011 | java and [matlab] source co | |
| 21296750 | c++ | SIMA: simultaneous multiple alignment of LC/MS peak lists. | 2011 | a [C++] implement | |
| 21296749 | mathlab | LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data. | 2011 | mented as [matlab] software | |
| 21296748 | javascript | Gobe: an interactive, web-based tool for comparative genomic visualization. | 2011 | heets and [javascript] callback | |
| 21278367 | python | Easyfig: a genome comparison visualizer. | 2011 | yfig is a [python] applicati | |
| 21278191 | java | Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. | 2011 | dependent [java] and avail | |
| 21278190 | perl | A Ruby API to query the Ensembl database for genomic features. | 2011 | through a [perl] api for a | |
| 21278188 | java | PiNGO: a Cytoscape plugin to find candidate genes in biological networks. | 2011 | en-source [java] package u | |
| 21278185 | perl | Quality control and preprocessing of metagenomic datasets. | 2011 | mented in [perl] and can b | |
| 21269502 | r | VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. | 2011 | agram, an [R package] that enab | |
| 21266444 | python | Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. | 2011 | a [python] package i | |
| 21261974 | java | PileLine: a toolbox to handle genome position information in next-generation sequencing studies. | 2011 | coded in [java] and run o | |
| 21258065 | mathlab | Computational refinement of post-translational modifications predicted from tandem mass spectrometry. | 2011 | mented in [matlab] and is fr | |
| 21258062 | r | HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. | 2011 | en in the [R language] and freel | |
| 21258060 | perl | WIST: toolkit for rapid, customized LIMS development. | 2011 | mented in [perl] and may b | |
| 21245054 | r | BayesPeak--an R package for analysing ChIP-seq data. | 2011 | speak--an [R package] for analy | |
| 21245051 | c++ | Automated bond order assignment as an optimization problem. | 2011 | en-source [C++] lgpl libr | |
| 21210988 | java | The Musite open-source framework for phosphorylation-site prediction. | 2010 | -designed [java] applicati | |
| 21210987 | perl | ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. | 2010 | ended the [perl] suite ont | |
| 21210979 | java | The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. | 2010 | e of sql, [java], r, or ht | |
| 21210978 | python | An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators. | 2010 | intuitive [python] interface | |
| 21210978 | r | An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators. | 2010 | ed on the [R language], has beco | |
| 21210977 | python | interPopula: a Python API to access the HapMap Project dataset. | 2010 | popula: a [python] api to ac | |
| 21233169 | c++ | Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. | 2011 | mented in [C++] and suppo | |
| 21233168 | r | High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. | 2011 | an [R package] of bpbaac | |
| 21233166 | r | A pipeline for RNA-seq data processing and quality assessment. | 2011 | the [R package] is availa | |
| 21233165 | c++ | ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration. | 2011 | ess++: a [C++] objected- | |
| 21228048 | r | CNAmet: an R package for integrating copy number, methylation and expression data. | 2011 | namet: an [R package] for integ | |
| 21224286 | python | GPU accelerated biochemical network simulation. | 2011 | present a [python] package, | |
| 21217123 | r | Robust linear regression methods in association studies. | 2011 | from the [R package] kinship i | |
| 21217122 | c++ | A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. | 2011 | ritten in [C++] and is gp | |
| 21216779 | java | A Java API for working with PubChem datasets. | 2011 | a [java] api for w | |
| 21216776 | java | MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. | 2011 | ase and a [java] applicati | |
| 21216773 | java | A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies. | 2011 | a [java] program, | |
| 21208987 | r | flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data. | 2011 | phyto, an [R package] that perf | |
| 21208986 | java | MIRACH: efficient model checker for quantitative biological pathway models. | 2011 | ped using [java] and thus | |
| 21208982 | java | Tabix: fast retrieval of sequence features from generic TAB-delimited files. | 2011 | ary in c, [java], perl and | |
| 21208982 | python | Tabix: fast retrieval of sequence features from generic TAB-delimited files. | 2011 | perl and [python]. it is pa | |
| 21208982 | perl | Tabix: fast retrieval of sequence features from generic TAB-delimited files. | 2011 | c, java, [perl] and pytho | |
| 21199577 | r | MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. | 2011 | f perl, c [and R] programs | |
| 21199577 | perl | MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. | 2011 | isting of [perl], c and r | |
| 21193521 | c++ | Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. | 2011 | d in ansi [C++] and can b | |
| 21177328 | mathlab | Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes. | 2011 | a [matlab] implement | |
| 21172910 | mathlab | Functional integration of a metabolic network model and expression data without arbitrary thresholding. | 2011 | mented in [matlab] and requi | |
| 21169379 | java | Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data. | 2011 | the [java] applicati | |
| 21169378 | r | phangorn: phylogenetic analysis in R. | 2011 | is in the [R language]. previous | |
| 21169377 | c++ | ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. | 2011 | ritten in [C++] and perl. | |
| 21169377 | perl | ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. | 2011 | n c++ and [perl]. it runs | |
| 21159624 | r | Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA. | 2011 | xtensible [R package] that perf | |
| 21149343 | perl | When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks. | 2011 | the [perl] script fo | |
| 21149340 | java | Cytoscape 2.8: new features for data integration and network visualization. | 2011 | a desktop [java] applicati | |
| 21149278 | c++ | Exploring metabolic pathways in genome-scale networks via generating flux modes. | 2011 | e code in [C++] is availa | |
| 21148545 | c++ | SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks. | 2011 | mented in [C++], is easil | |
| 21148542 | c++ | SlideSort: all pairs similarity search for short reads. | 2011 | files and [C++] libraries | |
| 21134892 | r | Rseg--an R package to optimize segmentation of SNP array data. | 2011 | rseg--an [R package] to optimi | |
| 21134890 | r | Predicting in vitro drug sensitivity using Random Forests. | 2011 | en in the [R language] and will | |
| 21129181 | r | Merged consensus clustering to assess and improve class discovery with microarray data. | 2010 | scribe an [R package] containin | |
| 21127034 | mathlab | A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. | 2011 | the [matlab] code for | |
| 21127032 | c++ | MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. | 2011 | atlab and [C++] source co | |
| 21127032 | mathlab | MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. | 2011 | [matlab] and c++ s | |
| 21123224 | java | GLay: community structure analysis of biological networks. | 2010 | cytoscape [java] program, | |
| 21118823 | python | Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. | 2011 | [python] code for | |
| 21118515 | mathlab | Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. | 2010 | ethods. a [matlab] implement | |
| 21118506 | r | Preprocessing of gene expression data by optimally robust estimators. | 2010 | ed in the [R package] named rob | |
| 21115438 | java | Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. | 2011 | atlab and [java] as well a | |
| 21115438 | python | Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. | 2011 | including [python], matlab a | |
| 21115438 | mathlab | Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. | 2011 | g python, [matlab] and java | |
| 21115436 | mathlab | von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. | 2011 | -platform [matlab] extension | |
| 21092255 | java | Reticular alignment: a progressive corner-cutting method for multiple sequence alignment. | 2010 | am in the [java] programmi | |
| 21088029 | r | Efficient change point detection for genomic sequences of continuous measurements. | 2011 | n the new [R package] cumseg av | |
| 21081511 | python | GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. | 2011 | mented in [python] and runs | |
| 21076148 | perl | PLEXY: efficient target prediction for box C/D snoRNAs. | 2011 | the [perl] script pl | |
| 21075747 | r | QuACN: an R package for analyzing complex biological networks quantitatively. | 2011 | quacn: an [R package] for analy | |
| 21075742 | r | Inference of gene networks--application to Bifidobacterium. | 2011 | le at www.[Bioconductor].org and a | |
| 21073736 | r | Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection. | 2010 | ed in the [R package] aplcms: h | |
| 21062762 | mathlab | Inverse perturbation for optimal intervention in gene regulatory networks. | 2011 | the [matlab] code for | |
| 21044358 | r | Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. | 2010 | yb probes [and R] script ar | |
| 21050468 | r | Optimizing transformations for automated, high throughput analysis of flow cytometry data. | 2010 | ithin the [Bioconductor] flowcore | |
| 21045073 | r | dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. | 2011 | hod in an [R package], which ca | |
| 21037244 | java | Bayesian sampling of genomic rearrangement scenarios via double cut and join. | 2010 | mented in [java] 1.5 progr | |
| 21034480 | mathlab | Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. | 2010 | mented in [matlab] and suppo | |
| 20980271 | mathlab | Optimized data fusion for K-means Laplacian clustering. | 2011 | the [matlab] code of a | |
| 20973958 | c++ | BALL--biochemical algorithms library 1.3. | 2010 | extensive [C++] class lib | |
| 20971988 | perl | The GMOD Drupal bioinformatic server framework. | 2010 | n php and [perl]. freely a | |
| 20971985 | r | Generalized random set framework for functional enrichment analysis using primary genomics datasets. | 2011 | rt of the [R package] clean fro | |
| 20966004 | r | R/qtl: high-throughput multiple QTL mapping. | 2010 | atistical [language r], and is m | |
| 20946609 | perl | Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize. | 2010 | rver, and [perl] cgi scrip | |
| 20946604 | perl | A framework for automated enrichment of functionally significant inverted repeats in whole genomes. | 2010 | rience in [perl]. | |
| 20946598 | perl | Next generation models for storage and representation of microbial biological annotation. | 2010 | esources, [perl], c, and u | |
| 20959382 | java | MiRonTop: mining microRNAs targets across large scale gene expression studies. | 2010 | an online [java] web tool | |
| 20958996 | mathlab | Discover protein complexes in protein-protein interaction networks using parametric local modularity. | 2010 | mented in [matlab] and is fr | |
| 20956245 | perl | High-quality annotation of promoter regions for 913 bacterial genomes. | 2010 | mented in [perl] and suppo | |
| 20956244 | java | Interactive microbial genome visualization with GView. | 2010 | view is a [java] applicati | |
| 20956243 | c++ | SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. | 2010 | che2 is a [C++] program c | |
| 20950483 | mathlab | Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. | 2010 | ssspec, a [matlab] implement | |
| 20947524 | java | OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data. | 2010 | mented in [java], omicsana | |
| 20947523 | java | The SMARTCyp cytochrome P450 metabolism prediction server. | 2010 | smartcyp [java] program a | |
| 20942945 | mathlab | Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data. | 2010 | mented in [matlab]. the prop | |
| 20942913 | java | Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm. | 2010 | mented in [java] and a use | |
| 20937596 | java | Pre-calculated protein structure alignments at the RCSB PDB website. | 2010 | ttp://www.[biojava].org. a so | |
| 20929913 | mathlab | R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. | 2010 | lign. the [matlab] source co | |
| 20929911 | python | PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. | 2010 | ritten in [python]. installa | |
| 20926422 | perl | TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence. | 2010 | suite of [perl] scripts a | |
| 20926421 | python | MEDELLER: homology-based coordinate generation for membrane proteins. | 2010 | mented in [python], bash and | |
| 20926421 | bash | MEDELLER: homology-based coordinate generation for membrane proteins. | 2010 | n python, [bash] and perl | |
| 20926421 | perl | MEDELLER: homology-based coordinate generation for membrane proteins. | 2010 | bash and [perl] cgi for u | |
| 20926419 | java | GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. | 2010 | mented in [java] and is fr | |
| 20880956 | r | A statistical framework for Illumina DNA methylation arrays. | 2010 | [R package] lumiwclus | |
| 20871108 | java | SylArray: a web server for automated detection of miRNA effects from expression data. | 2010 | perl and [java] and also | |
| 20871108 | perl | SylArray: a web server for automated detection of miRNA effects from expression data. | 2010 | perl-cgi, [perl] and java | |
| 20861030 | r | Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. | 2010 | the [R package] girafe is | |
| 20861029 | java | FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. | 2010 | file, the [java] gui and s | |
| 20861028 | c++ | BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. | 2010 | ucky is a [C++] program t | |
| 20847220 | java | Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. | 2010 | with sun [java] 1.5 or la | |
| 20847218 | python | Ruffus: a lightweight Python library for computational pipelines. | 2010 | ghtweight [python] library f | |
| 20843356 | perl | Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. | 2010 | ritten in [perl]. | |
| 20837570 | perl | A unified index of sequence quality and contig overlap for DNA barcoding. | 2010 | a gpl [perl] script is | |
| 20834038 | r | Semi-supervised recursively partitioned mixture models for identifying cancer subtypes. | 2010 | rried out [using R] (http://w | |
| 20834037 | c++ | Reptile: representative tiling for short read error correction. | 2010 | mented in [C++] and is av | |
| 20829444 | java | The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports. | 2010 | roovy and [java], the web | |
| 20828413 | r | Multivariate Hawkes process models of the occurrence of regulatory elements. | 2010 | ble as an [R package] from http | |
| 20828407 | java | Next generation tools for genomic data generation, distribution, and visualization. | 2010 | tandalone [java] swing app | |
| 20823315 | mathlab | De-correlating expression in gene-set analysis. | 2010 | the [matlab] codes and | |
| 20823308 | c++ | RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. | 2010 | mented in [C++], and the | |
| 20823304 | mathlab | Integrating genome assemblies with MAIA. | 2010 | able as a [matlab] package a | |
| 20823298 | mathlab | Automated construction and analysis of the design space for biochemical systems. | 2010 | olbox for [matlab] is freely | |
| 20817744 | mathlab | Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. | 2010 | [matlab] code impl | |
| 20815925 | c++ | Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. | 2010 | mework in [C++] for analy | |
| 20813878 | mathlab | Global modeling of transcriptional responses in interaction networks. | 2010 | in r and [matlab] at http:/ | |
| 20810601 | c++ | CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. | 2010 | en source [C++] code buil | |
| 20810601 | r | CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. | 2010 | the [R package] cogaps an | |
| 20801914 | r | DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. | 2010 | dcgl: an [R package] for ident | |
| 20739311 | mathlab | TFInfer: a tool for probabilistic inference of transcription factor activities. | 2010 | n earlier [matlab] version, | |
| 20739307 | java | BioRuby: bioinformatics software for the Ruby programming language. | 2010 | ns on the [java] virtual m | |
| 20736340 | java | Deep and wide digging for binding motifs in ChIP-Seq data. | 2010 | _genetika [java] package: | |
| 20733064 | c++ | Improving performances of suboptimal greedy iterative biclustering heuristics via localization. | 2010 | s in leda [C++] library, | |
| 20733063 | python | OpenStructure: a flexible software framework for computational structural biology. | 2010 | + or in a [python] layer, me | |
| 20733063 | c++ | OpenStructure: a flexible software framework for computational structural biology. | 2010 | ritten in [C++] with a cl | |
| 20709689 | java | QuantProReloaded: quantitative analysis of microspot immunoassays. | 2010 | in r and [java] and is op | |
| 20709689 | r | QuantProReloaded: quantitative analysis of microspot immunoassays. | 2010 | loaded is [written in R] and java | |
| 20704747 | perl | TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. | 2010 | ascca, a [perl] controlle | |
| 20702402 | java | Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. | 2010 | abase and [java] applicati | |
| 20702399 | mathlab | Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci. | 2010 | mented in [matlab] (the math | |
| 20702396 | mathlab | Cross-species queries of large gene expression databases. | 2010 | lts and a [matlab] implement | |
| 20702395 | java | BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets. | 2010 | mented in [java], provided | |
| 20702394 | python | RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. | 2010 | ritten in [python] and micro | |
| 20696734 | perl | MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences. | 2010 | [perl] source co | |
| 20691053 | java | PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. | 2010 | n c++ and [java] is provid | |
| 20691053 | c++ | PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. | 2010 | e code in [C++] and java | |
| 20688976 | r | A framework for oligonucleotide microarray preprocessing. | 2010 | ed on the [Bioconductor] principle | |
| 20685957 | c++ | SPRINT: side-chain prediction inference toolbox for multistate protein design. | 2010 | the full [C++] source co | |
| 20673335 | java | OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data. | 2010 | ritten in [java]. openchro | |
| 20671149 | r | ExpressionView--an interactive viewer for modules identified in gene expression data. | 2010 | iew is an [R package] that prov | |
| 20671148 | r | Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data. | 2010 | buted via [Bioconductor] under gnu | |
| 20667133 | r | Data reduction for spectral clustering to analyze high throughput flow cytometry data. | 2010 | thm as an [R package] is freely | |
| 20660295 | r | A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. | 2010 | tions. an [R package] named ggr | |
| 20656902 | javascript | Cytoscape Web: an interactive web-based network browser. | 2010 | pt with a [javascript] api and i | |
| 20651112 | perl | Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry. | 2010 | tation in [perl] for analy | |
| 20647521 | java | PathwayAccess: CellDesigner plugins for pathway databases. | 2010 | espective [java] applicati | |
| 20639410 | mathlab | On reverse engineering of gene interaction networks using time course data with repeated measurements. | 2010 | [matlab] code and | |
| 20637081 | r | R-Gada: a fast and flexible pipeline for copy number analysis in association studies. | 2010 | ent a new [R package], that int | |
| 20634205 | r | RPPanalyzer: Analysis of reverse-phase protein array data. | 2010 | ge on the [CRAN] platform | |
| 20631160 | mathlab | Probabilistic analysis of gene expression measurements from heterogeneous tissues. | 2010 | ritten in [matlab], and are | |
| 20628076 | java | PriorsEditor: a tool for the creation and use of positional priors in motif discovery. | 2010 | (requires [java] 1.6). the | |
| 20628074 | perl | OWL2Perl: creating Perl modules from OWL class definitions. | 2010 | creating [perl] modules f | |
| 20628073 | java | BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. | 2010 | mented in [java] and suppo | |
| 20628070 | r | Logic Forest: an ensemble classifier for discovering logical combinations of binary markers. | 2010 | ilable on [CRAN], http://c | |
| 20624783 | r | genoPlotR: comparative gene and genome visualization in R. | 2010 | dependent [R package], availabl | |
| 20624777 | java | Analyzing taxonomic classification using extensible Markov models. | 2010 | mented in [java] and suppo | |
| 20624289 | r | Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. | 2010 | 8 decoys ['R'] us decoy | |
| 20610611 | r | ROAST: rotation gene set tests for complex microarray experiments. | 2010 | on in the [Bioconductor] package l | |
| 20605930 | r | CNVineta: a data mining tool for large case-control copy number variation datasets. | 2010 | ineta, an [R package] for rapid | |
| 20598126 | r | A flexible R package for nonnegative matrix factorization. | 2010 | flexible [R package] for nonne | |
| 20595460 | r | mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits. | 2010 | mbmdr: an [R package] for explo | |
| 20591907 | python | ABC-SysBio--approximate Bayesian computation in Python with GPU support. | 2010 | tation in [python] with gpu | |
| 20587705 | r | Mining metabolic pathways through gene expression. | 2010 | an [R package] containin | |
| 20576627 | c++ | MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. | 2010 | ritten in [C++], is freel | |
| 20576626 | r | Single feature polymorphism detection using recombinant inbred line microarray expression data. | 2010 | the [R package] 'dipsfp' | |
| 20576622 | r | Cassis: detection of genomic rearrangement breakpoints. | 2010 | perl [and R] scripts a | |
| 20576622 | perl | Cassis: detection of genomic rearrangement breakpoints. | 2010 | [perl] and r scr | |
| 20565748 | java | Computing and visually analyzing mutual information in molecular co-evolution. | 2010 | mented in [java] and free | |
| 20562450 | c | Bridges: a tool for identifying local similarities in long sequences. | 2010 | ed in the [C programming] language | |
| 20562416 | python | Manipulation of FASTQ data with Galaxy. | 2010 | mented in [python] and has b | |
| 20562414 | java | Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. | 2010 | ed in the [java] language | |
| 20554691 | mathlab | Causal relationship inference for a large-scale cellular network. | 2010 | the [matlab] files for | |
| 20554688 | c++ | A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals. | 2010 | ferences) [C++] software, | |
| 20551135 | r | JAMIE: joint analysis of multiple ChIP-chip experiments. | 2010 | evelop an [R package] jamie to | |
| 20551134 | java | Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. | 2010 | and-alone [java] applicati | |
| 20550700 | c++ | Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. | 2010 | mented in [C++], using th | |
| 20546611 | java | Accessing the SEED genome databases via Web services API: tools for programmers. | 2010 | thon, and [java]. | |
| 20546611 | python | Accessing the SEED genome databases via Web services API: tools for programmers. | 2010 | as perl, [python], and java | |
| 20546611 | perl | Accessing the SEED genome databases via Web services API: tools for programmers. | 2010 | s such as [perl], python, | |
| 20538724 | c++ | Testing multiple gene interactions by the ordered combinatorial partitioning method in case-control studies. | 2010 | [C++] program i | |
| 20537149 | java | mu-CS: an extension of the TM4 platform to manage Affymetrix binary data. | 2010 | and as a [java] standalon | |
| 20534127 | r | FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. | 2010 | ctsnp: an [R package] to link s | |
| 20534127 | perl | FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. | 2010 | suite of [perl] scripts t | |
| 20529941 | python | Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. | 2010 | en in the [python] programmi | |
| 20529915 | mathlab | A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. | 2010 | uest as a [matlab] code pack | |
| 20529905 | mathlab | Efficient identification of identical-by-descent status in pedigrees with many untyped individuals. | 2010 | mented in [matlab] and is fr | |
| 20529902 | python | Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. | 2010 | mented by [python] and r. al | |
| 20529902 | r | Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. | 2010 | by python [and R]. all sour | |
| 20529900 | mathlab | Inferring combinatorial association logic networks in multimodal genome-wide screens. | 2010 | the [matlab] code of t | |
| 20529895 | java | SuperTriplets: a triplet-based supertree approach to phylogenomics. | 2010 | nline and [java] standalon | |
| 20529889 | r | ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. | 2010 | en-source [R package] acne, whi | |
| 20529363 | mathlab | L2-norm multiple kernel learning and its application to biomedical data fusion. | 2010 | the [matlab] code of a | |
| 20525223 | mathlab | poolMC: smart pooling of mRNA samples in microarray experiments. | 2010 | eloped in [matlab]. a proof- | |
| 20519286 | r | Structure-based variable selection for survival data. | 2010 | matlab [and R] code are | |
| 20519286 | mathlab | Structure-based variable selection for survival data. | 2010 | [matlab] and r cod | |
| 20519285 | perl | A computational genomics pipeline for prokaryotic sequencing projects. | 2010 | nation of [perl], bourne s | |
| 20513665 | java | SLIMS--a user-friendly sample operations and inventory management system for genotyping labs. | 2010 | ped using [java] 1.6.0, s, | |
| 20511363 | java | geWorkbench: an open source platform for integrative genomics. | 2010 | en source [java] desktop a | |
| 20509870 | python | Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. | 2010 | packages: [python], rpy and | |
| 20505005 | java | A UIMA wrapper for the NCBO annotator. | 2010 | mented in [java] for suppo | |
| 20505002 | perl | Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. | 2010 | nloadable [perl] script ar | |
| 20505000 | java | DA 1.0: parameter estimation of biological pathways using data assimilation approach. | 2010 | ped using [java] and thus | |
| 20501552 | c | A parallel algorithm to compute chemical organizations in biological networks. | 2010 | standard [C programming] language | |
| 20492697 | java | A high-level 3D visualization API for Java and ImageJ. | 2010 | n api for [java] and image | |
| 20487547 | r | sdef: an R package to synthesize lists of significant features in related experiments. | 2010 | sdef: an [R package] to synthe | |
| 20487544 | perl | Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. | 2010 | nts using [perl] and a rel | |
| 20472542 | python | The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. | 2010 | rce code, [python] bindings | |
| 20472541 | perl | Classification of DNA sequences using Bloom filters. | 2010 | aster 1.6 [perl] module ca | |
| 20472540 | java | Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming. | 2010 | en in the [java] computer | |
| 20462443 | mathlab | A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems. | 2010 | coded in [matlab], which im | |
| 20462408 | r | TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. | 2010 | -platform [R package] aroma.cn, | |
| 20459813 | perl | eHive: an artificial intelligence workflow system for genomic analysis. | 2010 | agent, a [perl] script, q | |
| 20459804 | r | ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. | 2010 | akanno: a [Bioconductor] package t | |
| 20459647 | r | Odefy--from discrete to continuous models. | 2010 | box, sbml [and R] script fi | |
| 20459647 | mathlab | Odefy--from discrete to continuous models. | 2010 | uad, gna, [matlab] script fi | |
| 20457667 | r | Repitools: an R package for the analysis of enrichment-based epigenomic data. | 2010 | tools: an [R package] for the a | |
| 20453004 | mathlab | Discover regulatory DNA elements using chromatin signatures and artificial neural network. | 2010 | mented in [matlab]. the sour | |
| 20453003 | c++ | Arcadia: a visualization tool for metabolic pathways. | 2010 | ritten in [C++]. the sour | |
| 20439257 | c++ | A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. | 2010 | [C++] source co | |
| 20439256 | c++ | Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. | 2010 | mented in [C++] and inclu | |
| 20438641 | python | Partitioning of copy-number genotypes in pedigrees. | 2010 | with the [python] interpret | |
| 20435580 | python | The Genomedata format for storing large-scale functional genomics data. | 2010 | tation in [python] and c com | |
| 20429928 | c++ | WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. | 2010 | ng visual [C++] 2005 expr | |
| 20427518 | r | ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. | 2010 | software, [written in R], under gp | |
| 20427516 | python | Modeling RNA loops using sequence homology and geometric constraints. | 2010 | mented in [python], mysql an | |
| 20421198 | python | DendroPy: a Python library for phylogenetic computing. | 2010 | ndropy: a [python] library f | |
| 20418341 | r | CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. | 2010 | aliter: a [Bioconductor] package f | |
| 20418340 | r | FABIA: factor analysis for bicluster acquisition. | 2010 | ble as an [R package] on biocon | |
| 20416082 | python | BS Seeker: precise mapping for bisulfite sequencing. | 2010 | omes. the [python] program i | |
| 20413636 | java | PepC: proteomics software for identifying differentially expressed proteins based on spectral counting. | 2010 | mented in [java]. it has b | |
| 20413635 | python | HangOut: generating clean PSI-BLAST profiles for domains with long insertions. | 2010 | mented in [python] 2.3 and r | |
| 20412558 | r | BioPhysConnectoR: Connecting sequence information and biophysical models. | 2010 | with the [R package] biophysco | |
| 20410052 | python | Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets. | 2010 | ritten in [python] and r are | |
| 20410052 | r | Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets. | 2010 | in python [and R] are avail | |
| 20410051 | c++ | Supersplat--spliced RNA-seq alignment. | 2010 | mented in [C++], superspl | |
| 20400454 | c++ | HIV classification using the coalescent theory. | 2010 | mented in [C++] and the s | |
| 20398407 | r | Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. | 2010 | arr is an [R package] that cove | |
| 20395285 | r | Picante: R tools for integrating phylogenies and ecology. | 2010 | vironment [written in R] and c, re | |
| 20385730 | r | Quality assessment of protein model-structures using evolutionary conservation. | 2010 | ious perl [and R] scripts u | |
| 20385730 | perl | Quality assessment of protein model-structures using evolutionary conservation. | 2010 | a [perl] implement | |
| 20385013 | java | web cellHTS2: a web-application for the analysis of high-throughput screening data. | 2010 | upporting [java] 1.5.0 can | |
| 20378558 | r | BoolNet--an R package for generation, reconstruction and analysis of Boolean networks. | 2010 | olnet--an [R package] for gener | |
| 20378557 | python | A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. | 2010 | vailable. [python] code and | |
| 20378555 | java | Correction of sequencing errors in a mixed set of reads. | 2010 | the [java] source co | |
| 20375112 | mathlab | Multilevel support vector regression analysis to identify condition-specific regulatory networks. | 2010 | he ml-svr [matlab] package c | |
| 20375111 | r | partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction. | 2010 | dsa as an [R package]. | |
| 20371495 | r | Modular analysis of gene expression data with R. | 2010 | oduce two [Bioconductor] software | |
| 20370922 | java | A highly efficient multi-core algorithm for clustering extremely large datasets. | 2010 | ed of our [java] based alg | |
| 20363732 | java | Streamlining the construction of large-scale dynamic models using generic kinetic equations. | 2010 | e code in [java], is avail | |
| 20363730 | java | ACCUSA--accurate SNP calling on draft genomes. | 2010 | rammed in [java] 6 and run | |
| 20363728 | r | Supervised normalization of microarrays. | 2010 | an [R package] called sn | |
| 20346105 | java | Moara: a Java library for extracting and normalizing gene and protein mentions. | 2010 | moara: a [java] library f | |
| 20338898 | r | EBImage--an R package for image processing with applications to cellular phenotypes. | 2010 | image--an [R package] for image | |
| 20307295 | java | In silico fragmentation for computer assisted identification of metabolite mass spectra. | 2010 | es and as [java] library. | |
| 20299327 | java | ArchSchema: a tool for interactive graphing of related Pfam domain architectures. | 2010 | hema is a [java] web start | |
| 20299326 | java | HALO--a Java framework for precise transcript half-life determination. | 2010 | halo--a [java] framework | |
| 20298548 | mathlab | Gene regulatory networks modelling using a dynamic evolutionary hybrid. | 2010 | nted in a [matlab] toolbox a | |
| 20230624 | java | RNAstructure: software for RNA secondary structure prediction and analysis. | 2010 | ritten in [java], and new | |
| 20230624 | c++ | RNAstructure: software for RNA secondary structure prediction and analysis. | 2010 | ibrary of [C++] classes f | |
| 20223837 | mathlab | Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. | 2010 | a [matlab] implement | |
| 20223834 | r | Integrative mixture of experts to combine clinical factors and gene markers. | 2010 | ed in the [R package] integrati | |
| 20215462 | mathlab | Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. | 2010 | the [matlab] code of t | |
| 20214778 | java | Mayday--integrative analytics for expression data. | 2010 | ways. as [java] program, | |
| 20214776 | mathlab | SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. | 2010 | y coupled [matlab] scripts t | |
| 20208069 | c++ | Genome-wide synteny through highly sensitive sequence alignment: Satsuma. | 2010 | mented in [C++] on linux. | |
| 20207696 | perl | Filtering error from SOLiD Output. | 2010 | ritten in [perl] and runs | |
| 20122197 | c++ | A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. | 2010 | a [C++] implement | |
| 20193060 | perl | The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. | 2010 | ackage of [perl] modules f | |
| 20189937 | mathlab | Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations. | 2010 | the [matlab] implement | |
| 20185407 | c++ | ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules. | 2010 | ghtweight [C++] library t | |
| 20181285 | java | SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system. | 2010 | (sc) is a [java] solution | |
| 20179076 | r | GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. | 2010 | emsim: an [R package] for measu | |
| 20179074 | python | Domain adaptation for semantic role labeling in the biomedical domain. | 2010 | mented in [python] and c and | |
| 20176580 | c++ | An optimal experimental design approach to model discrimination in dynamic biochemical systems. | 2010 | mented in [C++] in the pa | |
| 20172942 | r | CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. | 2010 | d in perl [and R] and runs | |
| 20172942 | perl | CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. | 2010 | mented in [perl] and r and | |
| 20170493 | r | A statistical framework for differential network analysis from microarray data. | 2010 | tions. an [R package] of our te | |
| 20163737 | r | Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. | 2010 | otentials ['R'] us web-se | |
| 20156990 | r | Phybase: an R package for species tree analysis. | 2010 | ybase: an [R package] for speci | |
| 20147305 | mathlab | Estimating replicate time shifts using Gaussian process regression. | 2010 | [matlab] code for | |
| 20147302 | perl | Fast and SNP-tolerant detection of complex variants and splicing in short reads. | 2010 | ograms in [perl] are freel | |
| 20144191 | r | Testing the additional predictive value of high-dimensional molecular data. | 2010 | ed in the [R package] globalbo | |
| 20130031 | perl | Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase. | 2010 | ritten in [perl] and c and | |
| 20130030 | python | Identifying biologically relevant differences between metagenomic communities. | 2010 | [python] source co | |
| 20128918 | r | BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets. | 2010 | babar: an [R package] to simpli | |
| 20122279 | c++ | Multiple structure alignment and consensus identification for proteins. | 2010 | mented in [C++] and can b | |
| 20118117 | c++ | A fast and automated solution for accurately resolving protein domain architectures. | 2010 | mented in [C++] and compi | |
| 20110278 | c++ | BEDTools: a flexible suite of utilities for comparing genomic features. | 2010 | ritten in [C++]. source c | |
| 20110277 | r | A hidden Ising model for ChIP-chip data analysis. | 2010 | ttp://www.[Bioconductor].org/. | |
| 20106819 | c++ | invertFREGENE: software for simulating inversions in population genetic data. | 2010 | [C++] source co | |
| 20106815 | perl | iMotifs: an integrated sequence motif visualization and analysis environment. | 2010 | s for the [perl], ruby, r | |
| 20105306 | python | Biana: a software framework for compiling biological interactions and analyzing networks. | 2010 | iana is a [python] framework | |
| 20097915 | mathlab | WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data. | 2010 | reader: a [matlab] program f | |
| 20096121 | r | NeatMap--non-clustering heat map alternatives in R. | 2010 | map is an [R package] designed | |
| 20089513 | r | rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments. | 2010 | en source [R package], rmat, th | |
| 20081222 | java | Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. | 2010 | dely used [java] software | |
| 20080510 | java | NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. | 2010 | and-alone [java] applicati | |
| 20080509 | r | pegas: an R package for population genetics with an integrated-modular approach. | 2010 | pegas: an [R package] for popul | |
| 20080508 | c++ | MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes. | 2010 | eloped in [C++] using the | |
| 20078892 | java | OLS dialog: an open-source front end to the ontology lookup service. | 2010 | created a [java] front end | |
| 20074382 | mathlab | LucidDraw: efficiently visualizing complex biochemical networks within MATLAB. | 2010 | ks within [matlab]. | |
| 20071372 | java | BamView: viewing mapped read alignment data in the context of the reference sequence. | 2010 | teractive [java] applicati | |
| 20070885 | python | ETE: a python Environment for Tree Exploration. | 2010 | ete: a [python] environme | |
| 20061306 | python | PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. | 2010 | contains [python] bindings | |
| 20056731 | r | CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. | 2010 | r with an [R package] for consu | |
| 20053276 | python | PyMix--the python mixture package--a tool for clustering of heterogeneous biological data. | 2010 | ymix--the [python] mixture p | |
| 20040588 | r | GWAF: an R package for genome-wide association analyses with family data. | 2010 | gwaf: an [R package] for genom | |
| 20040587 | r | Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects. | 2010 | able from [CRAN] (http://c | |
| 20031972 | r | DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. | 2010 | ment. the [R package] is availa | |
| 20028515 | java | A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. | 2009 | available [java] implement | |
| 20028515 | r | A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. | 2009 | in matlab [and R] by liu et | |
| 20028515 | mathlab | A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. | 2009 | al. using [matlab]. also, ba | |
| 20021670 | python | Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway. | 2009 | kage, the [python] environme | |
| 20015393 | c | TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. | 2009 | functions [written in C] for speed | |
| 20015393 | r | TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. | 2009 | search--a [Bioconductor] package f | |
| 20007740 | c++ | Tmod: toolbox of motif discovery. | 2010 | eloped in [C++] with the | |
| 20007253 | r | PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. | 2010 | pcit: an [R package] for weigh | |
| 20003544 | java | CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome. | 2009 | d in both [java] applicati | |
| 20003429 | java | Graphle: Interactive exploration of large, dense graphs. | 2009 | teractive [java] applet. t | |
| 20003386 | mathlab | Survival prediction from clinico-genomic models--a comparative study. | 2009 | ion data. [matlab] code for | |
| 20003283 | r | An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). | 2009 | en-source [R package] betr is a | |
| 19996165 | mathlab | Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. | 2010 | [matlab] code for | |
| 19996163 | c++ | HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences. | 2010 | mented in [C++] and suppo | |
| 19965880 | mathlab | DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets. | 2010 | ported to [matlab] or .xls. | |
| 19958528 | java | Bioclipse 2: a scriptable integration platform for the life sciences. | 2009 | mented in [java] and suppo | |
| 19942587 | java | Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. | 2010 | a [java] webstart | |
| 19942584 | java | CMap3D: a 3D visualization tool for comparative genetic maps. | 2010 | ssing and [java]. binaries | |
| 19939831 | java | Expertomica Cells: analysis of cell monolayer development. | 2010 | mented in [java] 6 and sup | |
| 19933825 | java | EGAN: exploratory gene association networks. | 2010 | gan) is a [java] desktop a | |
| 19933824 | r | A personalized microRNA microarray normalization method using a logistic regression model. | 2010 | asets and [R package] are avail | |
| 19933823 | java | MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. | 2010 | in r and [java], is avail | |
| 19933593 | r | Joint estimation of DNA copy number from multiple platforms. | 2010 | the [R package] for mpcbs | |
| 19933163 | mathlab | Bayesian variable selection for disease classification using gene expression data. | 2010 | a free [matlab] code to p | |
| 19933161 | python | Annotation and merging of SBML models with semanticSBML. | 2010 | ritten in [python] and relea | |
| 19933158 | r | Pathway analysis using random forests with bivariate node-split for survival outcomes. | 2010 | [R package] pwayrfsur | |
| 19930695 | r | Regularized estimation of large-scale gene association networks using graphical Gaussian models. | 2009 | ed in the [R package] parcor , | |
| 19914921 | python | PyNAST: a flexible tool for aligning sequences to a template alignment. | 2010 | possible. [python] nearest a | |
| 19910308 | r | edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. | 2010 | edger: a [Bioconductor] package f | |
| 19880372 | java | Model aggregation: a building-block approach to creating large macromolecular regulatory networks. | 2009 | [java] implement | |
| 19880369 | c++ | MicroRazerS: rapid alignment of small RNA reads. | 2010 | the seqan [C++] library a | |
| 19880368 | r | MATICCE: mapping transitions in continuous character evolution. | 2010 | ge in the [R language] for mappi | |
| 19874609 | python | multiplierz: an extensible API based desktop environment for proteomics data analysis. | 2009 | igh-level [python] scripts, | |
| 19861356 | c | Estimating population haplotype frequencies from pooled SNP data using incomplete database information. | 2009 | rce codes [written in C] (using gn | |
| 19861354 | mathlab | Computational protein profile similarity screening for quantitative mass spectrometry experiments. | 2010 | a [matlab] toolbox i | |
| 19860866 | mathlab | Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB. | 2009 | mented in [matlab]. | |
| 19855105 | r | DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. | 2010 | egseq: an [R package] for ident | |
| 19828085 | mathlab | A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection. | 2009 | code, as [matlab] scripts, | |
| 19828078 | perl | The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections. | 2009 | relies on [perl] scripts a | |
| 19828075 | perl | Extraction, integration and analysis of alternative splicing and protein structure distributed information. | 2009 | system of [perl] scripts h | |
| 19828071 | perl | A Perl procedure for protein identification by Peptide Mass Fingerprinting. | 2009 | a [perl] procedure | |
| 19850754 | r | The gputools package enables GPU computing in R. | 2010 | gputools [R package] is availa | |
| 19849862 | perl | Direct calibration of PICKY-designed microarrays. | 2009 | files and [perl] programs | |
| 19832995 | mathlab | Classification and biomarker identification using gene network modules and support vector machines. | 2009 | rrays.the [matlab] version o | |
| 19832968 | java | Magallanes: a web services discovery and automatic workflow composition tool. | 2009 | dependent [java] library o | |
| 19811691 | python | Exploratory visual analysis of conserved domains on multiple sequence alignments. | 2009 | ritten in [python] and using | |
| 19811679 | r | NATbox: a network analysis toolbox in R. | 2009 | ox in the [language r] that hous | |
| 19814779 | r | Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions. | 2009 | on of the [R package] nem ava | |
| 19811632 | mathlab | Generation of Gene Ontology benchmark datasets with various types of positive signal. | 2009 | coded in [matlab] and is fr | |
| 19808880 | r | HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R. | 2009 | d through [Bioconductor] or at htt | |
| 19808877 | r | Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. | 2009 | n in perl [and R], for simu | |
| 19808877 | perl | Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. | 2009 | ritten in [perl] and r, fo | |
| 19808875 | java | Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. | 2009 | mented in [java] utilizing | |
| 19776214 | java | SimCT: a generic tool to visualize ontology-based relationships for biological objects. | 2009 | specific [java] applet de | |
| 19773336 | mathlab | Bayesian detection of non-sinusoidal periodic patterns in circadian expression data. | 2009 | [matlab] software | |
| 19773334 | python | MOODS: fast search for position weight matrix matches in DNA sequences. | 2009 | operl and [biopython] toolkits. | |
| 19773334 | c++ | MOODS: fast search for position weight matrix matches in DNA sequences. | 2009 | ritten in [C++], with bin | |
| 19773334 | perl | MOODS: fast search for position weight matrix matches in DNA sequences. | 2009 | e popular [bioperl] and biopy | |
| 19751523 | r | Exploratory and inferential analysis of gene cluster neighborhood graphs. | 2009 | nsions of [R package] gcexplore | |
| 19747395 | javascript | ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites. | 2009 | ser-based [javascript] applicati | |
| 19744993 | javascript | QuickGO: a web-based tool for Gene Ontology searching. | 2009 | mented in [javascript], ajax and | |
| 19734153 | c | Bi-correlation clustering algorithm for determining a set of co-regulated genes. | 2009 | developed [using C] and visua | |
| 19734151 | java | Saint: a lightweight integration environment for model annotation. | 2009 | rted. the [java] source co | |
| 19720676 | java | Identification of genes involved in the same pathways using a Hidden Markov Model-based approach. | 2009 | [java] source co | |
| 19713416 | c++ | A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. | 2009 | [C++] source co | |
| 19713415 | mathlab | ERNEST: a toolbox for chemical reaction network theory. | 2009 | lbox is a [matlab] package w | |
| 19712446 | java | QPCR: Application for real-time PCR data management and analysis. | 2009 | web-based [java] applicati | |
| 19706745 | r | integrOmics: an R package to unravel relationships between two omics datasets. | 2009 | omics: an [R package] to unrave | |
| 19706743 | r | digeR: a graphical user interface R package for analyzing 2D-DIGE data. | 2009 | interface [R package] for analy | |
| 19706742 | mathlab | Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics. | 2009 | a [matlab] implement | |
| 19706180 | java | Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. | 2009 | ment kit: [java] tool kit | |
| 19698124 | c++ | MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering. | 2009 | well. the [C++] code and | |
| 19698094 | python | p3d--Python module for structural bioinformatics. | 2009 | this the [python] scripting | |
| 19696046 | java | PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains. | 2009 | requires [java], is avail | |
| 19696044 | c++ | Metabolite and reaction inference based on enzyme specificities. | 2009 | atlab and [C++] code is f | |
| 19696044 | mathlab | Metabolite and reaction inference based on enzyme specificities. | 2009 | [matlab] and c++ c | |
| 19689961 | java | CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data. | 2009 | ritten in [java]. | |
| 19689961 | c++ | CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data. | 2009 | ritten in [C++], while th | |
| 19689956 | python | CEAS: cis-regulatory element annotation system. | 2009 | the ceas [python] package i | |
| 19687029 | java | SnoopCGH: software for visualizing comparative genomic hybridization data. | 2009 | ritten in [java] and is av | |
| 19679825 | r | Stability and aggregation of ranked gene lists. | 2009 | available [Bioconductor] package g | |
| 19671693 | r | Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach. | 2009 | th matlab [and R] code that | |
| 19671693 | mathlab | Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach. | 2009 | both [matlab] and r cod | |
| 19671691 | java | T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. | 2009 | mented in [java], the prog | |
| 19661241 | r | R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. | 2009 | the crlmm [Bioconductor] package i | |
| 19656385 | java | Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. | 2009 | ritten in [java], and can | |
| 19654119 | r | ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. | 2009 | rtread: a [Bioconductor] package f | |
| 19654115 | r | Multiple testing in genome-wide association studies via hidden Markov models. | 2009 | an [R package] plis has | |
| 19654113 | java | The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. | 2009 | mented in [java] that supp | |
| 19653903 | mathlab | Generating rate equations for complex enzyme systems by a computer-assisted systematic method. | 2009 | athml and [matlab] output fi | |
| 19648135 | r | Gene ranking and biomarker discovery under correlation. | 2009 | ed in the [R package] 'st', whi | |
| 19646231 | java | sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures. | 2009 | xtensible [java] applicati | |
| 19640299 | r | CLEAN: CLustering Enrichment ANalysis. | 2009 | an add-on [R package] and can b | |
| 19628503 | mathlab | Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages. | 2009 | the [matlab] code for | |
| 19628502 | r | Moderated effect size and P-value combinations for microarray meta-analyses. | 2009 | an [R package] metama is | |
| 19620098 | perl | Benchmarking homology detection procedures with low complexity filters. | 2009 | [perl] scripts f | |
| 19607672 | perl | OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. | 2009 | ritten in [perl] and runs | |
| 19605418 | c++ | DiProGB: the dinucleotide properties genome browser. | 2009 | mented in [C++] and suppo | |
| 19602528 | mathlab | Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach. | 2009 | [matlab] scripts w | |
| 19589155 | r | puma: a Bioconductor package for propagating uncertainty in microarray analysis. | 2009 | puma: a [Bioconductor] package f | |
| 19578173 | python | FRED--a framework for T-cell epitope detection. | 2009 | mented in [python] in a modu | |
| 19578040 | c++ | TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration. | 2009 | xtensible [C++] software | |
| 19570806 | c++ | k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage. | 2009 | ritten in [C++]. | |
| 19561337 | java | HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. | 2009 | ritten in [java], supports | |
| 19561019 | r | A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. | 2009 | resent an [R package] ('massarr | |
| 19558728 | mathlab | DOTcvpSB, a software toolbox for dynamic optimization in systems biology. | 2009 | ritten in [matlab] and provi | |
| 19534756 | perl | The Mycoplasma conjunctivae genome sequencing, annotation and analysis. | 2009 | ected via [perl] scripts. | |
| 19534753 | java | RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences. | 2009 | dependent [java] program f | |
| 19534749 | java | A bioinformatics knowledge discovery in text application for grid computing. | 2009 | ritten in [java] on globus | |
| 19534746 | java | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. | 2009 | separate [java] applicati | |
| 19534737 | mathlab | 'Brukin2D': a 2D visualization and comparison tool for LC-MS data. | 2009 | built in [matlab] 7.4, whic | |
| 19542152 | java | SHREC: a short-read error correction method. | 2009 | en-source [java] implement | |
| 19538731 | r | designGG: an R-package and web tool for the optimal design of genetical genomics experiments. | 2009 | igngg, an [R package] for desig | |
| 19528086 | r | PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables. | 2009 | able as a [Bioconductor] package f | |
| 19528083 | java | De novo transcriptome assembly with ABySS. | 2009 | mented in [java] using the | |
| 19528083 | c++ | De novo transcriptome assembly with ABySS. | 2009 | mented in [C++]. the para | |
| 19505947 | c++ | Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. | 2009 | a [C++] implement | |
| 19505945 | c++ | trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. | 2009 | ritten in [C++], it is po | |
| 19505944 | mathlab | Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. | 2009 | lable for [matlab] and the p | |
| 19505942 | r | Importing ArrayExpress datasets into R/Bioconductor. | 2009 | from the [Bioconductor] project a | |
| 19505940 | java | Identifying the topology of protein complexes from affinity purification assays. | 2009 | a [java] implement | |
| 19497936 | perl | ABACAS: algorithm-based automatic contiguation of assembled sequences. | 2009 | mented in [perl] and is fr | |
| 19497932 | perl | Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. | 2009 | mented in [perl] and relie | |
| 19486540 | c | Fpocket: an open source platform for ligand pocket detection. | 2009 | en in the [C programming] language, | |
| 19478022 | perl | Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. | 2009 | [perl] and hyphy | |
| 19478016 | java | Identifying novel constrained elements by exploiting biased substitution patterns. | 2009 | nted in a [java] software | |
| 19478010 | java | Efficient exact motif discovery. | 2009 | mented in [java]. it can b | |
| 19477986 | c++ | Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. | 2009 | a [C++] implement | |
| 19477983 | mathlab | Fewer permutations, more accurate P-values. | 2009 | the [matlab] code can | |
| 19468055 | r | NTAP: for NimbleGen tiling array ChIP-chip data analysis. | 2009 | d in perl [and R] and can b | |
| 19468055 | perl | NTAP: for NimbleGen tiling array ChIP-chip data analysis. | 2009 | mented in [perl] and r and | |
| 19468054 | r | rtracklayer: an R package for interfacing with genome browsers. | 2009 | layer: an [R package] for inter | |
| 19468053 | java | Using chemical organization theory for model checking. | 2009 | ata and a [java] applet to | |
| 19463149 | r | Differential splicing using whole-transcript microarrays. | 2009 | ble as an [R package]. | |
| 19460889 | python | An active registry for bioinformatics web services. | 2009 | with php, [python], mysql an | |
| 19447787 | r | Gradient lasso for Cox proportional hazards model. | 2009 | [R package] glcoxph i | |
| 19442304 | r | flowClust: a Bioconductor package for automated gating of flow cytometry data. | 2009 | eloped an [R package] called fl | |
| 19439563 | java | Apollo: a community resource for genome annotation editing. | 2009 | ollo is a [java] applicati | |
| 19435744 | perl | Generating linkage mapping files from Affymetrix SNP chip data. | 2009 | agen is a [perl] tool that | |
| 19435742 | mathlab | Robust synthetic biology design: stochastic game theory approach. | 2009 | oolbox in [matlab]. finally, | |
| 19420051 | r | RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions. | 2009 | ble as an [R package] from cran | |
| 19414529 | r | apLCMS--adaptive processing of high-resolution LC/MS data. | 2009 | ted in an [R package] aplcms, w | |
| 19401401 | java | baobabLUNA: the solution space of sorting by reversals. | 2009 | mented in [java] is freely | |
| 19401399 | python | Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets. | 2009 | mented in [python], lisp, r | |
| 19398451 | r | penalizedSVM: a R-package for feature selection SVM classification. | 2009 | d. in the [R package] 'penalize | |
| 19398447 | r | GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. | 2009 | dependent [R package] available | |
| 19389734 | c++ | MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. | 2009 | the [C++] source co | |
| 19389732 | python | KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. | 2009 | the [python] source co | |
| 19376826 | java | A stochastic model for the evolution of metabolic networks with neighbor dependence. | 2009 | ampler in [java] is availa | |
| 19376823 | c++ | A local multiple alignment method for detection of non-coding RNA sequences. | 2009 | the [C++] source co | |
| 19374774 | r | Data-driven normalization strategies for high-throughput quantitative RT-PCR. | 2009 | are as an [R package] qpcrnorm | |
| 19369502 | java | Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. | 2009 | tten as a [java] applet, r | |
| 19358741 | r | flowCore: a Bioconductor package for high throughput flow cytometry. | 2009 | ls in the [R package] flowcore | |
| 19351618 | mathlab | Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. | 2009 | data and [matlab] code are | |
| 19349284 | r | Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. | 2009 | n source. [Bioconductor] 2.3 packa | |
| 19307241 | r | BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server. | 2009 | ed by the [Bioconductor] project, | |
| 19307239 | r | KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. | 2009 | in r and [Bioconductor]. | |
| 19304878 | python | Biopython: freely available Python tools for computational molecular biology and bioinformatics. | 2009 | available [python] tools for | |
| 19297349 | java | DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. | 2009 | en-source [java] das clien | |
| 19291295 | r | Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation. | 2009 | rough the [R package] kerfdr vi | |
| 19289448 | mathlab | Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. | 2009 | [matlab] code for | |
| 19289444 | python | GS2: an efficiently computable measure of GO-based similarity of gene sets. | 2009 | en-source [python] library. | |
| 19289443 | java | A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation. | 2009 | [java] classes a | |
| 19286834 | c++ | SimMLST: simulation of multi-locus sequence typing data under a neutral model. | 2009 | mented in [C++] and qt4 f | |
| 19286833 | c++ | Statistical detection of cooperative transcription factors with similarity adjustment. | 2009 | s well as [C++] source co | |
| 19286832 | c++ | A novel parallel approach to the likelihood-based estimation of admixture in population genetics. | 2009 | pi)-based [C++] implement | |
| 19279066 | c++ | Switching regulatory models of cellular stress response. | 2009 | atlab and [C++] code used | |
| 19279066 | mathlab | Switching regulatory models of cellular stress response. | 2009 | [matlab] and c++ c | |
| 19276151 | r | The tspair package for finding top scoring pair classifiers in R. | 2009 | cribe the [R package], tspair, | |
| 19269989 | java | PADRE: a package for analyzing and displaying reticulate evolution. | 2009 | en-source [java] program f | |
| 19269988 | c++ | RNATOPS-W: a web server for RNA structure searches of genomes. | 2009 | mand line [C++] software | |
| 19254921 | perl | DIYA: a bacterial annotation pipeline for any genomics lab. | 2009 | ritten in [perl], used for | |
| 19254356 | r | RGG: a general GUI Framework for R scripts. | 2009 | ogramming [language r] by adding | |
| 19251774 | perl | WSsas: a web service for the annotation of functional residues through structural homologues. | 2009 | ile and a [perl] client ar | |
| 19208175 | mathlab | Advanced analysis and visualization of gene copy number and expression data. | 2009 | tool is a [matlab] toolbox e | |
| 19244389 | r | Boosting for high-dimensional time-to-event data with competing risks. | 2009 | ed in the [R package] coxboost | |
| 19244386 | mathlab | BISEN: Biochemical Simulation Environment. | 2009 | ms in the [matlab] computing | |
| 19244385 | java | PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. | 2009 | requires [java] 5 or high | |
| 19237448 | r | PAnnBuilder: an R package for assembling proteomic annotation data. | 2009 | ilder: an [R package] for assem | |
| 19228411 | r | RankAggreg, an R package for weighted rank aggregation. | 2009 | ggreg, an [R package] for weigh | |
| 19225024 | r | gcExplorer: interactive exploration of gene clusters. | 2009 | t the new [R package] gcexplore | |
| 19223449 | javascript | OnTheFly: a tool for automated document-based text annotation, data linking and network generation. | 2009 | s to them [javascript] code to i | |
| 19218352 | javascript | CGAS: comparative genomic analysis server. | 2009 | nchronous [javascript] and xml ( | |
| 19213739 | c++ | Enumeration of condition-dependent dense modules in protein interaction networks. | 2009 | a [C++] implement | |
| 19211573 | c | STEM: species tree estimation using maximum likelihood for gene trees under coalescence. | 2009 | en in the [C language] to obtain | |
| 19200358 | r | EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. | 2009 | on r and [Bioconductor] packages | |
| 19193733 | java | Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree. | 2009 | active 3d [java] applicati | |
| 19193729 | c++ | QVALITY: non-parametric estimation of q-values and posterior error probabilities. | 2009 | lity is a [C++] program f | |
| 19188192 | c++ | Accurate identification of orthologous segments among multiple genomes. | 2009 | nted as a [C++] program. | |
| 19181685 | java | NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results. | 2009 | ast and a [java] applicati | |
| 19181683 | r | CORNA: testing gene lists for regulation by microRNAs. | 2009 | ble as an [R package] from http | |
| 19178723 | r | DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data. | 2009 | conductor [R package] that impl | |
| 19176559 | mathlab | A novel comprehensive wave-form MS data processing method. | 2009 | xample of [matlab] scripts u | |
| 19176556 | r | Parallelized prediction error estimation for evaluation of high-dimensional models. | 2009 | ed by the [R package] peperr, w | |
| 19176555 | r | A flexible rank-based framework for detecting copy number aberrations from array data. | 2009 | an [R package] rankcopy | |
| 19176553 | r | Testing significance relative to a fold-change threshold is a TREAT. | 2009 | ttp://www.[Bioconductor].org. | |
| 19176547 | c++ | A novel meta-analysis method exploiting consistency of high-throughput experiments. | 2009 | a [C++] implement | |
| 19171029 | r | Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring. | 2009 | wgeno, an [R package] for autom | |
| 19168913 | java | AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. | 2009 | the [java] code for | |
| 19166610 | javascript | Genome Projector: zoomable genome map with multiple views. | 2009 | nchronous [javascript] and xml ( | |
| 19154590 | mathlab | Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes. | 2009 | sets, the [matlab] code and | |
| 19154578 | r | Identifying differential exon splicing using linear models and correlation coefficients. | 2009 | of r and [Bioconductor] (bioclite | |
| 19151095 | java | Jalview Version 2--a multiple sequence alignment editor and analysis workbench. | 2009 | ghtweight [java] applet fo | |
| 19134227 | r | PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data. | 2009 | ctions in [Bioconductor] using a t | |
| 19114008 | r | WGCNA: an R package for weighted correlation network analysis. | 2008 | wgcna: an [R package] for weigh | |
| 19114001 | r | SPRINT: a new parallel framework for R. | 2008 | systems, [using R], but with | |
| 19112081 | mathlab | Differential dependency network analysis to identify condition-specific topological changes in biological networks. | 2009 | the ddn [matlab] toolbox a | |
| 19109877 | r | SimHap GUI: an intuitive graphical user interface for genetic association analysis. | 2008 | he simhap [R package], while pr | |
| 19106121 | r | arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. | 2009 | etrics--a [Bioconductor] package f | |
| 19106120 | python | AnnotationSketch: a genome annotation drawing library. | 2009 | ges ruby, [python] and lua. | |
| 19102758 | java | ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family. | 2008 | grid is a [java] applicati | |
| 19098028 | java | PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. | 2009 | e code, a [java].jar appli | |
| 19095699 | mathlab | Probabilistic assignment of formulas to mass peaks in metabolomics experiments. | 2009 | document, [matlab] code, dat | |
| 19087293 | perl | A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. | 2008 | cripts in [perl], bioperl, | |
| 19087285 | java | SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. | 2008 | e through [java] webstart | |
| 19074958 | r | rHVDM: an R package to predict the activity and targets of a transcription factor. | 2009 | rhvdm: an [R package] to predic | |
| 19073589 | r | SIMoNe: Statistical Inference for MOdular NEtworks. | 2009 | the [R package] simone (s | |
| 19073588 | mathlab | Matrix correlations for high-dimensional data: the modified RV-coefficient. | 2009 | the [matlab] m-files o | |
| 19068132 | java | The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. | 2008 | en source [java] applicati | |
| 19043077 | r | Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs. | 2009 | udy using [R language]. in our p | |
| 19040729 | r | Highly sensitive feature detection for high resolution LC/MS. | 2008 | into the [Bioconductor] r-package | |
| 19019849 | c++ | A multivariate test of association. | 2009 | a [C++] implement | |
| 19015130 | c++ | Prediction of translation initiation site for microbial genomes with TriTISA. | 2009 | the [C++] source co | |
| 19014642 | r | CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. | 2008 | ithin the [CRAN] project. | |
| 19014540 | r | A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data. | 2008 | e r-based [Bioconductor] and dchip | |
| 19014535 | perl | Extension of the COG and arCOG databases by amino acid and nucleotide sequences. | 2008 | s such as [perl] applied t | |
| 19014471 | r | Standardized high-throughput evaluation of cell-based compound screens. | 2008 | s a novel [R package] with a tc | |
| 18990722 | r | A novel signaling pathway impact analysis. | 2009 | ted as an [R package] available | |
| 18990721 | java | DNAPlotter: circular and linear interactive genome visualization. | 2009 | teractive [java] applicati | |
| 18984599 | java | TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. | 2009 | ed from a [java] graphical | |
| 18980677 | r | Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. | 2008 | from the [R package] archive c | |
| 18977780 | python | PConPy--a Python module for generating 2D protein maps. | 2008 | pconpy--a [python] module fo | |
| 18977779 | r | Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. | 2009 | ed in the [R language] and can b | |
| 18974169 | mathlab | Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. | 2008 | [matlab] code is a | |
| 18974073 | mathlab | Identifying molecular markers associated with classification of genotypes by External Logistic Biplots. | 2008 | the [matlab] code for | |
| 18959772 | r | minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information. | 2008 | from the [Bioconductor] website. | |
| 18957118 | java | MetaMine--a tool to detect and analyse gene patterns in their environmental context. | 2008 | mented in [java] and provi | |
| 18953044 | r | BASH: a tool for managing BeadArray spatial artefacts. | 2008 | beadarray [Bioconductor] package ( | |
| 18953044 | bash | BASH: a tool for managing BeadArray spatial artefacts. | 2008 | e present [bash], a tool f | |
| 18945685 | python | CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. | 2008 | of perl, [python] and r scr | |
| 18945685 | r | CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. | 2008 | l, python [and R] scripts, | |
| 18945685 | perl | CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. | 2008 | a set of [perl], python a | |
| 18940826 | java | QGene 4.0, an extensible Java QTL-analysis platform. | 2008 | xtensible [java] qtl-analy | |
| 18937846 | mathlab | Assessment of protein set coherence using functional annotations. | 2008 | networks. [matlab] code and | |
| 18925941 | r | CMA: a comprehensive Bioconductor package for supervised classification with high dimensional data. | 2008 | rehensive [Bioconductor] package f | |
| 18922808 | r | Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. | 2008 | [R package] to fit cm | |
| 18851737 | r | Probabilistic base calling of Solexa sequencing data. | 2008 | f 15%. an [R package] is provid | |
| 18842601 | c | A flexible forward simulator for populations subject to selection and demography. | 2008 | en in the [C programming] language) | |
| 18842599 | r | GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. | 2008 | dition, a [Bioconductor] package, | |
| 18842599 | mathlab | GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. | 2008 | esponding [matlab] implement | |
| 18842147 | mathlab | Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks. | 2008 | f f90 and [matlab] implement | |
| 18819939 | r | Identifying differentially expressed subnetworks with MMG. | 2008 | htm, from [CRAN], and has | |
| 18818216 | fortran | Bayesian learning of biological pathways on genomic data assimilation. | 2008 | the [fortran] source co | |
| 18817533 | java | Presenting and exploring biological pathways with PathVisio. | 2008 | etely new [java] implement | |
| 18812364 | java | Integrating and annotating the interactome using the MiMI plugin for cytoscape. | 2009 | hed using [java] webstart | |
| 18805798 | java | MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. | 2008 | ms-bid: a [java] package f | |
| 18803830 | java | GlycomeDB - integration of open-access carbohydrate structure databases. | 2008 | arge. the [java] applicati | |
| 18793458 | java | Clustering ionic flow blockade toggles with a mixture of HMMs. | 2008 | arning. a [java] implement | |
| 18796477 | python | tCal: transcriptional probability calculator using thermodynamic model. | 2008 | odel in a [python] module, ' | |
| 18790795 | r | Gene set enrichment analysis using linear models and diagnostics. | 2008 | ilable as [Bioconductor] package g | |
| 18789148 | mathlab | Increasing the efficiency of bacterial transcription simulations: when to exclude the genome without loss of accuracy. | 2008 | a simple [matlab] user inte | |
| 18784119 | java | F-Seq: a feature density estimator for high-throughput sequence tags. | 2008 | en in the [java] language | |
| 18784117 | fortran | Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. | 2008 | [fortran] 90 source | |
| 18776194 | java | STREAM: Static Thermodynamic REgulAtory Model of transcription. | 2008 | requires [java] version 5 | |
| 18757875 | c++ | PREDICT-2ND: a tool for generalized protein local structure prediction. | 2008 | required [C++] library i | |
| 18755046 | java | FERN - a Java framework for stochastic simulation and evaluation of reaction networks. | 2008 | fern - a [java] framework | |
| 18753155 | r | Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. | 2008 | hod in an [R package]. | |
| 18753153 | java | StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. | 2008 | ge in the [java] programmi | |
| 18721485 | perl | SynBlast: assisting the analysis of conserved synteny information. | 2008 | ritten in [perl] is availa | |
| 18718947 | r | Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. | 2008 | eemix: an [R package] for estim | |
| 18718946 | r | Eigen-R2 for dissecting variation in high-dimensional studies. | 2008 | lable via [Bioconductor]. | |
| 18718939 | r | Analyzing gene perturbation screens with nested effects models in R and bioconductor. | 2008 | en in the [R language] and freel | |
| 18710873 | r | Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited. | 2008 | .0 of the [R package] geneland. | |
| 18691414 | r | Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands. | 2008 | ilable at [CRAN] 1. this a | |
| 18689843 | mathlab | Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. | 2008 | ilable in [matlab] from http | |
| 18689838 | c++ | Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. | 2008 | [C++] code impl | |
| 18689828 | mathlab | Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. | 2008 | mented in [matlab] (mathwork | |
| 18689821 | python | Optimal spliced alignments of short sequence reads. | 2008 | n c++ and [python] are avail | |
| 18689821 | c++ | Optimal spliced alignments of short sequence reads. | 2008 | mented in [C++] and pytho | |
| 18689819 | java | Efficient representation and P-value computation for high-order Markov motifs. | 2008 | form of a [java] objectori | |
| 18689812 | mathlab | Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. | 2008 | the [matlab] code of t | |
| 18689808 | java | BioJava: an open-source framework for bioinformatics. | 2008 | nt in the [java] programmi | |
| 18687127 | r | Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data. | 2008 | n example [using R] and maxdb | |
| 18687127 | mathlab | Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data. | 2008 | as r and [matlab] require p | |
| 18682425 | perl | BLogo: a tool for visualization of bias in biological sequences. | 2008 | logo. the [perl] source co | |
| 18676972 | r | Predicting pathway membership via domain signatures. | 2008 | the [R package] gene2path | |
| 18676417 | java | Large-scale computation of elementary flux modes with bit pattern trees. | 2008 | tation in [java], with int | |
| 18676417 | mathlab | Large-scale computation of elementary flux modes with bit pattern trees. | 2008 | tion into [matlab] and suppo | |
| 18667443 | r | A fast Bayesian change point analysis for the segmentation of microarray data. | 2008 | duced the [R package] bcp (baye | |
| 18662925 | python | Mixture models for protein structure ensembles. | 2008 | the [python] source co | |
| 18641010 | c | Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data. | 2008 | a [C language] implement | |
| 18638416 | r | Assessing probe-specific dye and slide biases in two-color microarray data. | 2008 | ance. the [R package] lmgene wh | |
| 18635570 | r | mlegp: statistical analysis for computer models of biological systems using R. | 2008 | scribe an [R package], mlegp, t | |
| 18635567 | r | A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? | 2008 | ted in an [R package] called su | |
| 18635566 | java | ProCope--protein complex prediction and evaluation. | 2008 | rocope, a [java] software | |
| 18628290 | mathlab | Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein. | 2008 | [matlab] code is a | |
| 18621757 | mathlab | Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. | 2008 | all [matlab] files use | |
| 18620604 | java | PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies. | 2008 | ble file, [java] source co | |
| 18614583 | mathlab | Dynamical modeling and multi-experiment fitting with PottersWheel. | 2008 | gned as a [matlab] toolbox a | |
| 18613966 | r | A unified approach to false discovery rate estimation. | 2008 | from the [R package] archive c | |
| 18606607 | c++ | ProteoWizard: open source software for rapid proteomics tools development. | 2008 | ng modern [C++] technique | |
| 18599518 | java | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. | 2008 | running a [java] runtime e | |
| 18596077 | r | ChemmineR: a compound mining framework for R. | 2008 | ed by the [R package] chemminer | |
| 18593718 | java | BioMAJ: a flexible framework for databanks synchronization and processing. | 2008 | data. the [java] applicati | |
| 18593717 | r | PuReD-MCL: a graph-based PubMed document clustering methodology. | 2008 | e in perl [and R] are avail | |
| 18593717 | perl | PuReD-MCL: a graph-based PubMed document clustering methodology. | 2008 | e code in [perl] and r are | |
| 18586744 | mathlab | MicroRNA prediction with a novel ranking algorithm based on random walks. | 2008 | rammed in [matlab] on window | |
| 18586742 | c++ | Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. | 2008 | ervice. a [C++] implement | |
| 18586734 | python | Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. | 2008 | [python] and c sou | |
| 18586722 | mathlab | Protein complex identification by supervised graph local clustering. | 2008 | [matlab] implement | |
| 18586716 | python | Contact replacement for NMR resonance assignment. | 2008 | dependent [python] code. the | |
| 18586711 | mathlab | Combinatorial influence of environmental parameters on transcription factor activity. | 2008 | the [matlab] code is a | |
| 18586707 | mathlab | Alignment and classification of time series gene expression in clinical studies. | 2008 | [matlab] implement | |
| 18579568 | java | PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. | 2008 | the c and [java] programmi | |
| 18541052 | mathlab | Quantitative analysis of numerical solvers for oscillatory biomolecular system models. | 2008 | s. we use [matlab] numerical | |
| 18567917 | c++ | Database indexing for production MegaBLAST searches. | 2008 | the ncbi [C++] toolkit. | |
| 18544547 | r | Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value. | 2008 | available [R package] 'maclinic | |
| 18544546 | perl | Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. | 2008 | seed is a [perl] program t | |
| 18535082 | mathlab | Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. | 2008 | sifier in [matlab] is provid | |
| 18515276 | r | Sparse kernel methods for high-dimensional survival data. | 2008 | nse as an [R package] and can b | |
| 18513431 | mathlab | poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening. | 2008 | hits. the [matlab] codes for | |
| 18511468 | java | Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. | 2008 | izer is a [java] applicati | |
| 18511467 | c++ | Efficient functional clustering of protein sequences using the Dirichlet process. | 2008 | mented as [C++] software | |
| 18507856 | r | TileQC: a system for tile-based quality control of Solexa data. | 2008 | en in the [R language]. tileqc p | |
| 18501020 | perl | Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. | 2008 | nd (ii) a [perl] module, w | |
| 18501020 | javascript | Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. | 2008 | ritten in [javascript]. | |
| 18499696 | c++ | The Sleipnir library for computational functional genomics. | 2008 | sleipnir [C++] library i | |
| 18499695 | c | EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis. | 2008 | for emrf [written in C] is availa | |
| 18485197 | javascript | Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. | 2008 | mented in [javascript] within th | |
| 18482995 | r | qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. | 2008 | qpcr: an [R package] for sigmo | |
| 18480100 | java | Computing chemical organizations in biological networks. | 2008 | ata and a [java] implement | |
| 18477576 | perl | A distance metric for a class of tree-sibling phylogenetic networks. | 2008 | the [perl] package b | |
| 18474508 | c++ | DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. | 2008 | ritten in [C++]. | |
| 18474506 | java | Malin: maximum likelihood analysis of intron evolution in eukaryotes. | 2008 | and-alone [java] applicati | |
| 18474505 | java | FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA. | 2008 | and-alone [java] applicati | |
| 18474116 | perl | Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. | 2008 | ritten in [perl] and with | |
| 18467348 | r | lumi: a pipeline for processing Illumina microarray. | 2008 | lumi is a [Bioconductor] package e | |
| 18467347 | java | Microbial genotype-phenotype mapping by class association rule mining. | 2008 | de of the [java] implement | |
| 18467344 | c++ | PatMaN: rapid alignment of short sequences to large databases. | 2008 | the [C++] source co | |
| 18453554 | c++ | An efficient method to identify differentially expressed genes in microarray experiments. | 2008 | the [C++] code to i | |
| 18450812 | r | A correction for estimating error when using the Local Pooled Error Statistical Test. | 2008 | ed in the [R language] and can b | |
| 18450810 | c++ | quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. | 2008 | coded in [C++] using an | |
| 18447951 | java | Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory. | 2008 | optimized [java] implement | |
| 18445606 | java | jSquid: a Java applet for graphical on-line network exploration. | 2008 | jsquid: a [java] applet fo | |
| 18445289 | java | An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. | 2008 | teractive [java] applicati | |
| 18441000 | r | fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. | 2008 | versatile [R package] for estim | |
| 18440999 | c++ | MAMOT: hidden Markov modeling tool. | 2008 | mented in [C++], and is d | |
| 18430251 | perl | VariVis: a visualisation toolkit for variation databases. | 2008 | executing [perl] cgi scrip | |
| 18424458 | java | Fast grid layout algorithm for biological networks with sweep calculation. | 2008 | [java] implement | |
| 18416814 | mathlab | anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. | 2008 | eloped in [matlab] a general | |
| 18387211 | perl | Version VI of the ESTree db: an improved tool for peach transcriptome analysis. | 2008 | a [perl] modular p | |
| 18413327 | r | Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. | 2008 | nse as an [R package] on the co | |
| 18407922 | c | Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. | 2008 | developed [using C] and visua | |
| 18405375 | java | uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. | 2008 | ode in c, [java], and c#, | |
| 18405375 | python | uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. | 2008 | perl and [python] are provi | |
| 18405375 | perl | uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. | 2008 | tions for [perl] and pytho | |
| 18400774 | c++ | A system for generating transcription regulatory networks with combinatorial control of transcription. | 2008 | enco is a [C++] command l | |
| 18397895 | r | adegenet: a R package for the multivariate analysis of genetic markers. | 2008 | egenet: a [R package] for the m | |
| 18390879 | java | UniProtJAPI: a remote API for accessing UniProt data. | 2008 | created a [java] library n | |
| 18375965 | python | CompariMotif: quick and easy comparisons of sequence motifs. | 2008 | en source [python] modules u | |
| 18371228 | java | A perl package and an alignment tool for phylogenetic networks. | 2008 | veloped a [java] applet th | |
| 18371228 | perl | A perl package and an alignment tool for phylogenetic networks. | 2008 | a [perl] package a | |
| 18366796 | java | Chromhome: a rich internet application for accessing comparative chromosome homology maps. | 2008 | nterprise [java] platform | |
| 18356193 | mathlab | Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo. | 2008 | [matlab] code used | |
| 18353790 | perl | A suite of Perl modules for handling microarray data. | 2008 | suite of [perl] modules f | |
| 18344518 | r | Unequal group variances in microarray data analyses. | 2008 | [R package] to perfor | |
| 18344248 | mathlab | Fitting a geometric graph to a protein-protein interaction network. | 2008 | [matlab] code impl | |
| 18325927 | mathlab | Merging two gene-expression studies via cross-platform normalization. | 2008 | s and xpn [matlab] code are | |
| 18325106 | r | Empirical Bayes analysis of single nucleotide polymorphisms. | 2008 | le in the [R package] siggenes | |
| 18318917 | r | Normalization of oligonucleotide arrays based on the least-variant set of genes. | 2008 | ation. an [R package] called lv | |
| 18318908 | java | Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies. | 2008 | mented in [java] and can b | |
| 18312684 | java | A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation. | 2008 | a [java] applicati | |
| 18296463 | r | CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. | 2008 | atistical [language r]. we encou | |
| 18292114 | mathlab | MMG: a probabilistic tool to identify submodules of metabolic pathways. | 2008 | [matlab] code is a | |
| 18284666 | r | K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. | 2008 | or matlab [and R], licensed | |
| 18284666 | mathlab | K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. | 2008 | rithm for [matlab] and r, li | |
| 18267948 | mathlab | Complexity reduction of biochemical rate expressions. | 2008 | box 2 for [matlab], which is | |
| 18263642 | java | Interactive visualization software for exploring phylogenetic trees and clades. | 2008 | ste) is a [java] applicati | |
| 18252739 | r | ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. | 2008 | the [R package] italics ( | |
| 18252737 | java | LibSBML: an API library for SBML. | 2008 | mon lisp, [java], python, | |
| 18252737 | python | LibSBML: an API library for SBML. | 2008 | sp, java, [python], perl, ma | |
| 18252737 | c++ | LibSBML: an API library for SBML. | 2008 | iso c and [C++], provides | |
| 18252737 | perl | LibSBML: an API library for SBML. | 2008 | , python, [perl], matlab a | |
| 18252737 | mathlab | LibSBML: an API library for SBML. | 2008 | on, perl, [matlab] and octav | |
| 18251994 | java | The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences. | 2008 | se uses a [java] program t | |
| 18251993 | java | A comparison of common programming languages used in bioinformatics. | 2008 | c++, c#, [java], perl and | |
| 18251993 | python | A comparison of common programming languages used in bioinformatics. | 2008 | perl and [python]. | |
| 18251993 | c++ | A comparison of common programming languages used in bioinformatics. | 2008 | ted in c, [C++], c#, java | |
| 18251993 | perl | A comparison of common programming languages used in bioinformatics. | 2008 | c#, java, [perl] and pytho | |
| 18245128 | r | Using flowViz to visualize flow cytometry data. | 2008 | ble as an [R package] from the | |
| 18245126 | c++ | Model-based Bayesian clustering (MBBC). | 2008 | ox, r and [C++], taking a | |
| 18245126 | r | Model-based Bayesian clustering (MBBC). | 2008 | un the ox [and R] programs | |
| 18245124 | perl | ONTO-PERL: an API for supporting the development and analysis of bio-ontologies. | 2008 | ://search.[CPAN].org/dist/ | |
| 18238804 | java | Interoperability with Moby 1.0--it's better than sharing your toothbrush! | 2008 | perl and [java] code-base | |
| 18238804 | perl | Interoperability with Moby 1.0--it's better than sharing your toothbrush! | 2008 | upporting [perl] and java | |
| 18237431 | r | AWclust: point-and-click software for non-parametric population structure analysis. | 2008 | ted as an [R package]. the soft | |
| 18237374 | r | SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. | 2008 | es finder [using R]'mes to se | |
| 18227118 | java | Utility library for structural bioinformatics. | 2008 | ritten in [java] language | |
| 18227117 | r | Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. | 2008 | ithin the [Bioconductor] r-package | |
| 18227116 | java | TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers. | 2008 | xecutable [java] archive f | |
| 18221524 | perl | TOBFAC: the database of tobacco transcription factors. | 2008 | used the [perl] programmi | |
| 18221524 | javascript | TOBFAC: the database of tobacco transcription factors. | 2008 | mented in [javascript] and perl | |
| 18218657 | perl | Colorstock, SScolor, Ratón: RNA alignment visualization tools. | 2008 | scolor, a [perl] script th | |
| 18208605 | r | SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. | 2008 | tool and [R package] for gene | |
| 18205906 | perl | T2prhd: a tool to study the patterns of repeat evolution. | 2008 | nted in a [perl] script (t | |
| 18204060 | r | HCGene: a software tool to support the hierarchical classification of genes. | 2008 | the [R package] hcgene (h | |
| 18204055 | r | Estimation and assessment of raw copy numbers at the single locus level. | 2008 | en-source [R package] named aro | |
| 18204054 | r | Using repeated measurements to validate hierarchical gene clusters. | 2008 | oped in c [and R] languages | |
| 18203773 | r | Multiple testing on the directed acyclic graph of gene ontology. | 2008 | le on www.[Bioconductor].org. | |
| 18202028 | perl | The SGN comparative map viewer. | 2008 | oriented [perl], with a s | |
| 18201381 | r | Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. | 2008 | compliant [R package] 'annotati | |
| 18194961 | mathlab | Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. | 2008 | [matlab] code to i | |
| 18194537 | java | NestedMICA as an ab initio protein motif discovery tool. | 2008 | ritten in [java], is drive | |
| 18187444 | java | Effect of spatial distribution of T-Cells and HIV load on HIV progression. | 2008 | c++ and [java] have been | |
| 18187444 | c++ | Effect of spatial distribution of T-Cells and HIV load on HIV progression. | 2008 | [C++] and java | |
| 18187443 | mathlab | A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. | 2008 | [matlab] files for | |
| 18187441 | r | OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data. | 2008 | lierd: an [R package] for outli | |
| 18184687 | mathlab | A hybrid model for robust detection of transcription factor binding sites. | 2008 | a [matlab] implement | |
| 18184432 | c++ | SeqAn an efficient, generic C++ library for sequence analysis. | 2008 | , generic [C++] library f | |
| 18180239 | c++ | FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. | 2008 | includes [C++] implement | |
| 18177498 | r | Extending pathways based on gene lists using InterPro domain signatures. | 2008 | lable via [Bioconductor]. | |
| 18175769 | mathlab | Structural systems identification of genetic regulatory networks. | 2008 | the [matlab] code is a | |
| 18174185 | java | Automated programming for bioinformatics algorithm deployment. | 2008 | for most [java] bioinform | |
| 18154664 | javascript | Userscripts for the life sciences. | 2007 | ritten in [javascript]. informat | |
| 18086686 | r | affyGG: computational protocols for genetical genomics with Affymetrix arrays. | 2008 | s: (i) an [R package] providing | |
| 18086686 | perl | affyGG: computational protocols for genetical genomics with Affymetrix arrays. | 2008 | and (ii) [perl] scripts p | |
| 18056736 | c++ | Rfold: an exact algorithm for computing local base pairing probabilities. | 2008 | the [C++] source co | |
| 18056069 | java | Automated manipulation of systems biology models using libSBML within Taverna workflows. | 2008 | nd invoke [java] classes a | |
| 18056063 | r | Model-based deconvolution of genome-wide DNA binding. | 2008 | en-source [R package], includin | |
| 18042557 | mathlab | Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. | 2007 | [matlab] code avai | |
| 18037684 | r | RReportGenerator: automatic reports from routine statistical analysis using R. | 2008 | analysis [using R]. | |
| 18037683 | perl | Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. | 2008 | l and the [perl] scripts p | |
| 18034891 | java | Dendroscope: An interactive viewer for large phylogenetic trees. | 2007 | ritten in [java] 1.4 and i | |
| 18033794 | java | Analysis of a Gibbs sampler method for model-based clustering of gene expression data. | 2008 | ganesh, a [java] package f | |
| 18033791 | java | PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees. | 2008 | vizapi: a [java] api for t | |
| 18028540 | c | Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. | 2007 | ecodon is [written in C], can run | |
| 18025006 | r | Estimating node degree in bait-prey graphs. | 2008 | rough the [Bioconductor] project ( | |
| 18024976 | r | GlobalANCOVA: exploration and assessment of gene group effects. | 2008 | ttp://www.[Bioconductor].org) offe | |
| 18024975 | mathlab | Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. | 2008 | tirelief. [matlab] source co | |
| 18024972 | mathlab | A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. | 2008 | [matlab] code is a | |
| 18024473 | r | Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. | 2008 | tree cut [R package] that impl | |
| 18006550 | r | GEIGER: investigating evolutionary radiations. | 2008 | en in the [R language], to descr | |
| 18006546 | c++ | GWAsimulator: a rapid whole-genome simulation program. | 2008 | the [C++] source co | |
| 18005434 | r | Novel definition files for human GeneChips based on GeneAnnot. | 2007 | uidelines [and R] code, cdf | |
| 18005402 | perl | A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification. | 2007 | tegies. a [perl] script th | |
| 18003646 | mathlab | Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra. | 2008 | the [matlab] implement | |
| 18003643 | r | Vbmp: variational Bayesian Multinomial Probit Regression for multi-class classification in R. | 2008 | bmp is an [R package] for gauss | |
| 17997843 | r | BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips. | 2007 | conductor [R package] that impl | |
| 17996092 | java | An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. | 2007 | esign and [java] as a plat | |
| 17989096 | r | Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. | 2008 | intact, a [Bioconductor] package t | |
| 17989094 | java | Hierarchical tree snipping: clustering guided by prior knowledge. | 2007 | a [java] package i | |
| 17977888 | python | Moment invariants as shape recognition technique for comparing protein binding sites. | 2007 | [python] code is a | |
| 17977884 | mathlab | Ensemble learning of genetic networks from time-series expression data. | 2007 | the [matlab] codes are | |
| 17977882 | java | PfamAlyzer: domain-centric homology search. | 2007 | yzer is a [java] applet th | |
| 17947255 | c++ | i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. | 2008 | tains the [C++] source co | |
| 17947255 | perl | i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. | 2008 | s various [perl] scripts a | |
| 17941985 | java | Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. | 2007 | mented in [java]. the soft | |
| 17939871 | mathlab | Local Renyi entropic profiles of DNA sequences. | 2007 | eloped in [matlab] m-code, t | |
| 17937818 | java | MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. | 2007 | lization, [java] and java3 | |
| 17937790 | r | Large scale statistical inference of signaling pathways from RNAi and microarray data. | 2007 | from the [Bioconductor] homepage. | |
| 17933854 | r | MDQC: a new quality assessment method for microarrays based on quality control reports. | 2007 | able from [Bioconductor]. | |
| 17921494 | java | Biclustering as a method for RNA local multiple sequence alignment. | 2007 | mented in [java]. source c | |
| 17921491 | c++ | Improved BLAST searches using longer words for protein seeding. | 2007 | cbi c and [C++] toolkit c | |
| 17921172 | r | I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. | 2007 | ed in the [R package] farms (ww | |
| 17906332 | r | A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R. | 2007 | conductor [and R]. | |
| 17903289 | r | Graphs in molecular biology. | 2007 | rough the [Bioconductor] project a | |
| 17900369 | r | A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. | 2007 | ble as an [R package], metaarra | |
| 17895273 | perl | TandTRAQ: an open-source tool for integrated protein identification and quantitation. | 2007 | tandtraq [perl] scripts a | |
| 17893085 | java | TreeSnatcher: coding trees from images. | 2007 | ui-driven [java] applicati | |
| 17881408 | r | Moderated statistical tests for assessing differences in tag abundance. | 2007 | an [R package] can be ac | |
| 17880681 | c | A cross-species alignment tool (CAT). | 2007 | plemented [using C] scripts a | |
| 17877799 | mathlab | A framework for significance analysis of gene expression data using dimension reduction methods. | 2007 | le, and a [matlab] toolbox ( | |
| 17875544 | r | oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. | 2007 | liar with [R language]. | |
| 17872912 | mathlab | Graph-based consensus clustering for class discovery from gene expression data. | 2007 | [matlab] source co | |
| 17855420 | javascript | AVIS: AJAX viewer of interactive signaling networks. | 2007 | nchronous [javascript] with xml) | |
| 17855418 | java | Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. | 2007 | and-alone [java] program v | |
| 17855418 | mathlab | Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. | 2007 | sbml and [matlab] m-files. | |
| 17854506 | javascript | OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. | 2007 | nchronous [javascript] and xml) | |
| 17846036 | c++ | Clustal W and Clustal X version 2.0. | 2007 | ritten in [C++]. this wil | |
| 17846035 | c++ | A genotype calling algorithm for the Illumina BeadArray platform. | 2007 | the [C++] executabl | |
| 17827205 | mathlab | Exploiting sample variability to enhance multivariate analysis of microarray data. | 2007 | [matlab] script fi | |
| 17768165 | r | An error model for protein quantification. | 2007 | matlab [and R] code is a | |
| 17768165 | mathlab | An error model for protein quantification. | 2007 | [matlab] and r cod | |
| 17767709 | r | GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. | 2007 | tool and [R package] for gene | |
| 17725829 | java | Integrated network reconstruction, visualization and analysis using YANAsquare. | 2007 | ackage in [java]. it is fu | |
| 17725821 | perl | MaxAlign: maximizing usable data in an alignment. | 2007 | able as a [perl] stand-alo | |
| 17720985 | mathlab | Metal reduction kinetics in Shewanella. | 2007 | mented in [matlab]. it consi | |
| 17720982 | r | A comparison of background correction methods for two-colour microarrays. | 2007 | le in the [R package] limma (sm | |
| 17716377 | java | Protein structural similarity search by Ramachandran codes. | 2007 | and-alone [java] program t | |
| 17683598 | java | TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy. | 2007 | ritten in [java] as a plug | |
| 17683565 | r | Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. | 2007 | ithin the [R package] gimmr whi | |
| 17678535 | perl | PepBank--a database of peptides based on sequence text mining and public peptide data sources. | 2007 | ell as on [CPAN] (http://w | |
| 17660206 | r | Robust smooth segmentation approach for array CGH data analysis. | 2007 | the [R package] smoothseg | |
| 17660205 | r | sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets. | 2007 | from weka [and R] packages | |
| 17655753 | r | msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. | 2007 | several c [and R] programs | |
| 17655753 | perl | msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. | 2007 | un with a [perl] front-en | |
| 17646351 | java | Homology search for genes. | 2007 | the [java] implement | |
| 17646350 | java | In search of lost introns. | 2007 | the [java] implement | |
| 17646338 | r | From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. | 2007 | grams are [written in R] and avail | |
| 17646331 | java | Continuous hidden process model for time series expression experiments. | 2007 | a [java] implement | |
| 17646320 | java | Functional annotation of regulatory pathways. | 2007 | mented in [java] and is av | |
| 17646311 | r | Nested effects models for high-dimensional phenotyping screens. | 2007 | le in the [R package] 'nem' fro | |
| 17646288 | mathlab | Kernel-based data fusion for gene prioritization. | 2007 | the [matlab] code used | |
| 17644558 | java | GSEA-P: a desktop application for Gene Set Enrichment Analysis. | 2007 | on of the [java] based sof | |
| 17626633 | java | A novel ensemble learning method for de novo computational identification of DNA binding sites. | 2007 | nterface, [java] source co | |
| 17623703 | c++ | HMMoC--a compiler for hidden Markov models. | 2007 | efficient [C++] implement | |
| 17623700 | r | RefPlus: an R package extending the RMA Algorithm. | 2007 | fplus: an [R package] extending | |
| 17605777 | mathlab | Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. | 2007 | lable for [matlab] and will | |
| 17599937 | perl | CASVM: web server for SVM-based prediction of caspase substrates cleavage sites. | 2007 | ritten in [perl] and hoste | |
| 17599935 | mathlab | Improving gene quantification by adjustable spot-image restoration. | 2007 | mented in [matlab] (the math | |
| 17599926 | python | QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. | 2007 | pygr (the [python] graph dat | |
| 17594490 | java | Constructing a meaningful evolutionary average at the phylogenetic center of mass. | 2007 | design. a [java] implement | |
| 17594490 | r | Constructing a meaningful evolutionary average at the phylogenetic center of mass. | 2007 | atistical [language r]. | |
| 17594472 | r | Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. | 2007 | en-source [R package] ringo tha | |
| 17586828 | r | beadarray: R classes and methods for Illumina bead-based data. | 2007 | from the [Bioconductor] web page | |
| 17586826 | mathlab | BiVisu: software tool for bicluster detection and visualization. | 2007 | eloped in [matlab] and is av | |
| 17586549 | java | Evaporative cooling feature selection for genotypic data involving interactions. | 2007 | ritten in [java], is freel | |
| 17586546 | r | Annotation-based distance measures for patient subgroup discovery in clinical microarray studies. | 2007 | ovide the [R package] adsplit a | |
| 17586543 | r | Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. | 2007 | ted in an [R package] 'correp' | |
| 17584939 | mathlab | Precise protein quantification based on peptide quantification using iTRAQ. | 2007 | 2.2. the [matlab] scripts o | |
| 17584922 | python | Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of molecular clock assumption with 3D visualization. | 2007 | cientific [python] to genera | |
| 17559666 | perl | Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. | 2007 | :nexus: a [perl] api for t | |
| 17553857 | r | Predicting survival from microarray data--a comparative study. | 2007 | matlab [and R] code for | |
| 17553857 | mathlab | Predicting survival from microarray data--a comparative study. | 2007 | [matlab] and r cod | |
| 17550911 | java | Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models. | 2007 | available [java] program: | |
| 17545183 | java | OBO-Edit--an ontology editor for biologists. | 2007 | mented in [java], obo-edit | |
| 17540683 | c++ | Simple and fast alignment of metabolic pathways by exploiting local diversity. | 2007 | mented in [C++] as a user | |
| 17540682 | mathlab | Bayesian modelling of shared gene function. | 2007 | ement and [matlab] code are | |
| 17537755 | python | PALMA: mRNA to genome alignments using large margin algorithms. | 2007 | n c++ and [python] are avail | |
| 17537755 | c++ | PALMA: mRNA to genome alignments using large margin algorithms. | 2007 | mented in [C++] and pytho | |
| 17537750 | java | StrBioLib: a Java library for development of custom computational structural biology applications. | 2007 | biolib: a [java] library f | |
| 17519250 | r | Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. | 2007 | atistical [language r] and is av | |
| 17519247 | c++ | The evolutionary forest algorithm. | 2007 | a [C++] implement | |
| 17519018 | r | GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products. | 2007 | ithin the [CRAN] project. | |
| 17510172 | perl | Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. | 2007 | the [perl] script im | |
| 17496320 | r | GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. | 2007 | (geo) and [Bioconductor]. | |
| 17496317 | java | OBO to OWL: a protege OWL tab to read/save OBO ontologies. | 2007 | verter, a [java] tool to c | |
| 17495999 | r | WilcoxCV: an R package for fast variable selection in cross-validation. | 2007 | coxcv: an [R package] for fast | |
| 17495998 | java | MutationFinder: a high-performance system for extracting point mutation mentions from text. | 2007 | perl and [java]. mutation | |
| 17495998 | python | MutationFinder: a high-performance system for extracting point mutation mentions from text. | 2007 | ilable in [python], perl and | |
| 17495998 | perl | MutationFinder: a high-performance system for extracting point mutation mentions from text. | 2007 | n python, [perl] and java. | |
| 17495997 | mathlab | PLMaddon: a power-law module for the Matlab SBToolbox. | 2007 | e for the [matlab] sbtoolbox | |
| 17495995 | java | Nucleotide composition string selection in HIV-1 subtyping using whole genomes. | 2007 | the [java] executabl | |
| 17488757 | c++ | Madeline 2.0 PDE: a new program for local and web-based pedigree drawing. | 2007 | -oriented [C++] and relea | |
| 17485432 | r | CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. | 2007 | calib: a [Bioconductor] package f | |
| 17485430 | r | Assessment of survival prediction models based on microarray data. | 2007 | ted in an [R package] called pe | |
| 17483508 | mathlab | Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. | 2007 | ritten in [matlab], can be d | |
| 17483503 | java | PQuad--a visual analysis platform for proteomic data exploration of microbial organisms. | 2007 | requires [java] 1.5 and h | |
| 17477871 | r | A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array. | 2007 | ted in an [R package] faseg, wh | |
| 17470480 | java | SPACER: identification of cis-regulatory elements with non-contiguous critical residues. | 2007 | a [java] 1.4 imple | |
| 17468121 | mathlab | Alignment of molecular networks by integer quadratic programming. | 2007 | [matlab] code and | |
| 17463028 | mathlab | Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer. | 2007 | e code in [matlab] is access | |
| 17463026 | java | iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. | 2007 | -platform [java] executabl | |
| 17459965 | perl | TOPD/FMTS: a new software to compare phylogenetic trees. | 2007 | the [perl] source co | |
| 17459963 | c++ | GENOME: a rapid coalescent-based whole genome simulator. | 2007 | ogram and [C++] source co | |
| 17459961 | c++ | Murlet: a practical multiple alignment tool for structural RNA sequences. | 2007 | the [C++] source co | |
| 17445272 | perl | CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. | 2007 | using the [perl] programmi | |
| 17445272 | javascript | CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. | 2007 | mented in [javascript] and perl | |
| 17430557 | perl | ESTuber db: an online database for Tuber borchii EST sequences. | 2007 | developed [perl] scripts. | |
| 17428344 | python | Flexible mapping of homology onto structure with homolmapper. | 2007 | ritten in [python] to ensure | |
| 17425803 | perl | BranchClust: a phylogenetic algorithm for selecting gene families. | 2007 | mented in [perl] with the | |
| 17394657 | r | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. | 2007 | ible with [Bioconductor], affymetr | |
| 17392333 | java | Cyclone: java-based querying and computing with Pathway/Genome databases. | 2007 | xtensible [java] object ap | |
| 17392331 | mathlab | Modeling sequence-sequence interactions for drug response. | 2007 | ritten in [matlab] can be do | |
| 17389034 | java | Modeling biochemical transformation processes and information processing with Narrator. | 2007 | mented as [java] software | |
| 17384430 | java | MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets. | 2007 | mpp is a [java] applicati | |
| 17384428 | java | Semantic Web Service provision: a realistic framework for Bioinformatics programmers. | 2007 | existing [java] applicati | |
| 17384426 | perl | GoSh: a web-based database for goat and sheep EST sequences. | 2007 | e tags. a [perl] pipeline | |
| 17384020 | r | IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform. | 2007 | nted as a [R package] based on | |
| 17384017 | mathlab | SBML export interface for the systems biology toolbox for MATLAB. | 2007 | olbox for [matlab]. | |
| 17384016 | java | Mediante: a web-based microarray data manager. | 2007 | oped as a [j2ee] three-tie | |
| 17379692 | r | Domain-enhanced analysis of microarray data using GO annotations. | 2007 | e in r as [Bioconductor] packages, | |
| 17346331 | java | Orthology prediction at scalable resolution by phylogenetic tree analysis. | 2007 | eliminary [java] version o | |
| 17344241 | r | pcaMethods--a bioconductor package providing PCA methods for incomplete data. | 2007 | ethods--a [Bioconductor] package p | |
| 17344240 | r | Codelink: an R package for analysis of GE healthcare gene expression bioarrays. | 2007 | elink: an [R package] for analy | |
| 17344233 | java | BioGuideSRS: querying multiple sources with a user-centric perspective. | 2007 | stem with [java] 5.0. | |
| 17341494 | java | Comparative annotation of viral genomes with non-conserved gene structure. | 2007 | the [java] code is a | |
| 17341299 | java | SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). | 2007 | ritten in [java] using jco | |
| 17332022 | perl | NucPred--predicting nuclear localization of proteins. | 2007 | tion, the [perl] code is m | |
| 17332019 | c++ | COBALT: constraint-based alignment tool for multiple protein sequences. | 2007 | the ncbi [C++] toolkit. | |
| 17324941 | java | Multiple structural alignment and clustering of RNA sequences. | 2007 | mented in [java] and is, a | |
| 17324941 | perl | Multiple structural alignment and clustering of RNA sequences. | 2007 | ompanying [perl] scripts, | |
| 17324940 | java | Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager. | 2007 | ped using [java] and other | |
| 17316423 | java | Bioclipse: an open source workbench for chemo- and bioinformatics. | 2007 | ritten in [java] and based | |
| 17309895 | java | Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. | 2007 | en-source [java] plugin fo | |
| 17308338 | java | A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies. | 2007 | a new [java] interface | |
| 17282999 | c++ | Assessment of the probabilities for evolutionary structural changes in protein folds. | 2007 | system in [C++] and using | |
| 17280615 | java | NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. | 2007 | of a thin [java] client bu | |
| 17280615 | c++ | NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. | 2007 | n in ansi [C++]. the java | |
| 17277335 | c | Hardware acceleration of processing of mass spectrometric data for proteomics. | 2007 | algorithm [written in C], running | |
| 17267438 | mathlab | An ensemble approach to microarray data-based gene prioritization after missing value imputation. | 2007 | the [matlab] codes are | |
| 17267436 | r | SNPassoc: an R package to perform whole genome association studies. | 2007 | assoc: an [R package] to perfor | |
| 17244370 | java | GraphDNA: a Java program for graphical display of DNA composition analyses. | 2007 | aphdna: a [java] program f | |
| 17242030 | c++ | SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis. | 2007 | mented in [C++], for the | |
| 17237105 | c++ | A comparative genome approach to marker ordering. | 2007 | ftware in [C++], includin | |
| 17237103 | c++ | Simultaneous alignment and annotation of cis-regulatory regions. | 2007 | ine based [C++] implement | |
| 17237103 | perl | Simultaneous alignment and annotation of cis-regulatory regions. | 2007 | e provide [perl] scripts f | |
| 17237101 | c++ | Tandem repeats over the edit distance. | 2007 | mented in [C++], and the | |
| 17237073 | perl | ProServer: a simple, extensible Perl DAS server. | 2007 | xtensible [perl] das serve | |
| 17237072 | python | Biskit--a software platform for structural bioinformatics. | 2007 | -oriented [python] library t | |
| 17237071 | mathlab | SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB. | 2007 | olbox for [matlab]. | |
| 17237067 | mathlab | Inferring pairwise regulatory relationships from multiple time series datasets. | 2007 | [matlab] implement | |
| 17237065 | mathlab | Peak selection from MALDI-TOF mass spectra using ant colony optimization. | 2007 | erial and [matlab] scripts t | |
| 17237063 | c++ | Compressed suffix tree--a basis for genome-scale sequence analysis. | 2007 | the [C++] implement | |
| 17237060 | mathlab | Quick calculation for sample size while controlling false discovery rate with application to microarray analysis. | 2007 | a [matlab] code impl | |
| 17237056 | java | The ESID Online Database network. | 2007 | based on [java] 2 enterpr | |
| 17237045 | mathlab | Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models. | 2007 | sas and [matlab] codes are | |
| 17237038 | r | R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. | 2007 | able from [CRAN].r-project | |
| 17234643 | r | A faster circular binary segmentation algorithm for the analysis of array CGH data. | 2007 | ge of the [Bioconductor] project. | |
| 17234637 | r | snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. | 2007 | developed [R package] which pro | |
| 17233908 | java | AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. | 2007 | ped using [java] and runs | |
| 17224057 | r | Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. | 2007 | etrix and [Bioconductor] in early | |
| 17217518 | java | SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data. | 2006 | rehensive [java] interface | |
| 17217507 | c++ | Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data. | 2006 | g mpi and [C++] libraries | |
| 17204461 | r | SNPchip: R classes and methods for SNP array data. | 2007 | tion. the [R package] snpchip c | |
| 17204155 | c++ | FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data. | 2007 | hms, in a [C++] software | |
| 17199898 | c++ | TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. | 2007 | , and the [C++] and perl | |
| 17199898 | perl | TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. | 2007 | e c++ and [perl] sources o | |
| 17182699 | c++ | URec: a system for unrooted reconciliation. | 2007 | mented in [C++] and can b | |
| 17182698 | c++ | Robust prediction of consensus secondary structures using averaged base pairing probability matrices. | 2007 | the [C++] source co | |
| 17166856 | r | Segmentation and intensity estimation of microarray images using a gamma-t mixture model. | 2007 | mentation [R language] softwares | |
| 17166856 | mathlab | Segmentation and intensity estimation of microarray images using a gamma-t mixture model. | 2007 | mented in [matlab]. the matl | |
| 17166289 | java | The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases. | 2006 | ') in the [java] language | |
| 17158515 | mathlab | Quantitative performance metrics for robustness in circadian rhythms. | 2007 | orithm in [matlab] (mathwork | |
| 17158513 | r | GGtools: analysis of genetics of gene expression in bioconductor. | 2007 | ession in [Bioconductor]. | |
| 17145740 | c | cBrother: relaxing parental tree assumptions for Bayesian recombination detection. | 2007 | s a novel [C language] implement | |
| 17142814 | java | The automation of Nested Clade Phylogeographic Analysis. | 2007 | ritten in [java] and requi | |
| 17138590 | java | MotifScorer: using a compendium of microarrays to identify regulatory motifs. | 2007 | ritten in [java] and matla | |
| 17138590 | mathlab | MotifScorer: using a compendium of microarrays to identify regulatory motifs. | 2007 | java and [matlab], manual a | |
| 17138589 | java | Visualization of genomic aberrations using Affymetrix SNP arrays. | 2007 | dependent [java] applicati | |
| 17138585 | java | BioNetBuilder: automatic integration of biological networks. | 2007 | able as a [java] webstart, | |
| 17130137 | mathlab | Improved breast cancer prognosis through the combination of clinical and genetic markers. | 2007 | e.com and [matlab] codes are | |
| 17127677 | r | Mosclust: a software library for discovering significant structures in bio-molecular data. | 2007 | the [R package] mosclust | |
| 17121773 | mathlab | PrepMS: TOF MS data graphical preprocessing tool. | 2007 | files and [matlab] toolbox a | |
| 17118131 | c++ | Permutation test for periodicity in short time series data. | 2006 | a set of [C++] programs | |
| 17116249 | r | CoXpress: differential co-expression in gene expression data. | 2006 | press, an [R package] that allo | |
| 17105719 | mathlab | Detecting protein dissimilarities in multiple alignments using Bayesian variable selection. | 2007 | the [matlab] code for | |
| 17101042 | java | 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. | 2006 | ritten in [java] and there | |
| 17098774 | r | Using GOstats to test gene lists for GO term association. | 2007 | ble as an [R package] from the | |
| 17095514 | c | Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences. | 2006 | e code is [written in C] and distr | |
| 17092991 | java | Modular organization of protein interaction networks. | 2007 | orithm. a [java] program, | |
| 17092990 | r | Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. | 2007 | e program [written in R] is availa | |
| 17087823 | java | XML schemas for common bioinformatic data types and their application in workflow systems. | 2006 | them in a [java] library ( | |
| 17077099 | java | Towards clustering of incomplete microarray data without the use of imputation. | 2007 | ped using [java] language, | |
| 17068091 | c++ | Adding sequence context to a Markov background model improves the identification of regulatory elements. | 2006 | our [C++] program i | |
| 17064411 | perl | CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. | 2006 | ritten in [perl] and in a | |
| 17060354 | java | Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites. | 2006 | ses via a [java] program a | |
| 17059604 | perl | SNP-PHAGE--High throughput SNP discovery pipeline. | 2006 | ritten in [perl] and uses | |
| 17059595 | r | Goulphar: rapid access and expertise for standard two-color microarray normalization methods. | 2006 | using the [R language] and envir | |
| 17054794 | java | Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis. | 2006 | [java] gui for i | |
| 17054788 | java | inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons. | 2006 | ritten in [java] with bioj | |
| 17046977 | java | MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. | 2006 | ritten in [java] and is av | |
| 17038344 | c++ | Parameter estimation using Simulated Annealing for S-system models of biochemical networks. | 2007 | ritten in [C++] is availa | |
| 17038193 | java | A Fisheye Viewer for microarray-based gene expression data. | 2006 | mented in [java] so that i | |
| 17038191 | java | MIMOX: a web tool for phage display based epitope mapping. | 2006 | view as a [java] applet to | |
| 17038191 | perl | MIMOX: a web tool for phage display based epitope mapping. | 2006 | coded in [perl] using mod | |
| 17032677 | java | ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies. | 2006 | ements. a [java] graphic u | |
| 17021156 | r | P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R. | 2006 | le as the [R package] 'pbatr' w | |
| 17005537 | r | BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network. | 2006 | array: an [R package] for const | |
| 17005535 | perl | CAPS: coevolution analysis using protein sequences. | 2006 | aps) is a [perl] based sof | |
| 17000750 | c++ | Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis. | 2006 | the [C++] applicati | |
| 16982708 | r | RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. | 2006 | nkprod: a [Bioconductor] package f | |
| 16966362 | mathlab | Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities. | 2006 | [matlab] code is a | |
| 16966359 | python | SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins. | 2006 | ritten in [python] to assist | |
| 16954144 | java | SEBINI: Software Environment for BIological Network Inference. | 2006 | html. the [java] source co | |
| 16953879 | java | A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls. | 2006 | ritten in [java], 2) a mys | |
| 16940322 | r | Bio3d: an R package for the comparative analysis of protein structures. | 2006 | bio3d: an [R package] for the c | |
| 16928738 | c++ | MARD: a new method to detect differential gene expression in treatment-control time courses. | 2006 | coded in [C++] and is av | |
| 16895932 | r | COPA--cancer outlier profile analysis. | 2006 | pa) in an [R package] (that we | |
| 16895923 | c++ | Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. | 2006 | [C++] source co | |
| 16882649 | c++ | Nemo: an evolutionary and population genetics programming framework. | 2006 | as both a [C++] programmi | |
| 16882648 | python | PYCHEM: a multivariate analysis package for python. | 2006 | ckage for [python]. | |
| 16882648 | mathlab | PYCHEM: a multivariate analysis package for python. | 2006 | ools like [matlab], pychem 2 | |
| 16882647 | r | Reliable gene signatures for microarray classification: assessment of stability and performance. | 2006 | [R package] at http:/ | |
| 16877754 | c++ | General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. | 2006 | ritten in [C++]. | |
| 16877753 | r | Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach. | 2006 | the [R package] of the da | |
| 16877752 | r | Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays. | 2006 | ent as an [R package] for the b | |
| 16873522 | mathlab | AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. | 2006 | nted in a [matlab] metalangu | |
| 16873504 | mathlab | Integrating copy number polymorphisms into array CGH analysis using a robust HMM. | 2006 | ritten in [matlab] is availa | |
| 16873460 | java | Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. | 2006 | ctave and [java] (with a g | |
| 16870933 | java | JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins. | 2006 | dependent [java] version a | |
| 16864592 | r | arrayQCplot: software for checking the quality of microarray data. | 2006 | developed [using R] and provi | |
| 16845144 | mathlab | Bayesian variable selection for the analysis of microarray data with censored outcomes. | 2006 | the [matlab] code for | |
| 16844712 | r | OrderedList--a bioconductor package for detecting similarity in ordered gene lists. | 2006 | edlist--a [Bioconductor] package f | |
| 16844709 | perl | SynView: a GBrowse-compatible approach to visualizing comparative genome data. | 2006 | ritten in [perl] and runs | |
| 16844707 | java | CART variance stabilization and regularization for high-throughput genomic data. | 2006 | ithin the [java] software | |
| 16844704 | mathlab | Gene selection in cancer classification using sparse logistic regression with Bayesian regularization. | 2006 | a [matlab] implement | |
| 16837522 | mathlab | Remote homology detection based on oligomer distances. | 2006 | e/thomas. [matlab] code for | |
| 16824223 | r | AMDA: an R package for the automated microarray data analysis. | 2006 | amda: an [R package] for the a | |
| 16820431 | java | VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. | 2006 | ritten in [java]. it can b | |
| 16820430 | mathlab | Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. | 2006 | form with [matlab] 7.1 (sp3) | |
| 16820429 | r | Probe-level measurement error improves accuracy in detecting differential gene expression. | 2006 | ted in an [R package] pplr. the | |
| 16820429 | mathlab | Probe-level measurement error improves accuracy in detecting differential gene expression. | 2006 | mented in [matlab]. both sof | |
| 16820428 | r | Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. | 2006 | le in the [Bioconductor] project. | |
| 16817977 | java | PROMPT: a protein mapping and comparison tool. | 2006 | ty of the [java] applicati | |
| 16809393 | c++ | An iterative refinement algorithm for consistency based multiple structural alignment methods. | 2006 | the [C++] code of t | |
| 16809388 | java | ET viewer: an application for predicting and visualizing functional sites in protein structures. | 2006 | ted using [java] to run ac | |
| 16809386 | r | Pathway analysis using random forests classification and regression. | 2006 | urce code [written in R] is availa | |
| 16792813 | r | PSMIX: an R package for population structure inference via maximum likelihood method. | 2006 | psmix: an [R package] for popul | |
| 16790057 | perl | AgdbNet - antigen sequence database software for bacterial typing. | 2006 | rsed by a [perl] cgi scrip | |
| 16787977 | mathlab | A lock-and-key model for protein-protein interactions. | 2006 | rithm (in [matlab] format) i | |
| 16787976 | python | Cleaver: software for identifying taxon specific restriction endonuclease recognition sites. | 2006 | that have [python] 2.3 and n | |
| 16787969 | r | Transcript mapping with high-density oligonucleotide tiling arrays. | 2006 | [R package] tilingarr | |
| 16782726 | java | Building chromosome-wide LD maps. | 2006 | coded in [java], which ru | |
| 16782725 | java | JCell--a Java-based framework for inferring regulatory networks from time series data. | 2006 | is a pure [java] applicati | |
| 16777905 | r | Robust estimation of the false discovery rate. | 2006 | of s-plus [and R] routines | |
| 16766560 | java | JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation. | 2006 | stributed [java] applicati | |
| 16766557 | java | SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides. | 2006 | seqvis, a [java] applicati | |
| 16766556 | mathlab | Transcriptome network component analysis with limited microarray data. | 2006 | olbox for [matlab] is availa | |
| 16762054 | java | Cell_motility: a cross-platform, open source application for the study of cell motion paths. | 2006 | en source [java] applicati | |
| 16740163 | java | AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. | 2006 | ritten in [java] we have p | |
| 16740163 | c | AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. | 2006 | g program [written in C] with a us | |
| 16731697 | mathlab | Metatool 5.0: fast and flexible elementary modes analysis. | 2006 | octave or [matlab] environme | |
| 16717070 | c | NETGEN: generating phylogenetic networks with diploid hybrids. | 2006 | netgen is [written in C] and is av | |
| 16716215 | r | Spatial normalization of array-CGH data. | 2006 | ed in the [R package] manor (mi | |
| 16709589 | mathlab | Independent component analysis-based penalized discriminant method for tumor classification using gene expression data. | 2006 | [matlab] scripts a | |
| 16709588 | java | Combo: a whole genome comparative browser. | 2006 | ritten in [java], runs on | |
| 16705015 | r | Combining multiple microarrays in the presence of controlling variables. | 2006 | programs [written in R] will be e | |
| 16700920 | java | Bounded search for de novo identification of degenerate cis-regulatory elements. | 2006 | ethods. a [java] implement | |
| 16682424 | r | PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer. | 2006 | from (www.[CRAN].r-project | |
| 16675467 | fortran | A mixture model with random-effects components for clustering correlated gene-expression profiles. | 2006 | a [fortran] program b | |
| 16643673 | mathlab | PDA: Pooled DNA analyzer. | 2006 | with the [matlab] language, | |
| 16640789 | java | JColorGrid: software for the visualization of biological measurements. | 2006 | orgrid, a [java] library a | |
| 16638137 | java | RNAmute: RNA secondary structure mutation analysis tool. | 2006 | teractive [java] applicati | |
| 16632491 | c++ | GeneRecon--a coalescent based tool for fine-scale association mapping. | 2006 | ritten in [C++] and schem | |
| 16632490 | mathlab | A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription. | 2006 | [matlab] code is a | |
| 16630347 | java | Exploration of biological network centralities with CentiBiN. | 2006 | rsions: a [java] web start | |
| 16623940 | r | Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. | 2006 | p and the [Bioconductor] packages | |
| 16611354 | mathlab | Integrative investigation of metabolic and transcriptomic data. | 2006 | oolbox in [matlab]. | |
| 16600045 | java | An interactive tool for visualization of relationships between gene expression profiles. | 2006 | ritten in [java], treebuil | |
| 16600027 | java | AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. | 2006 | rammed in [java]. | |
| 16595561 | java | ProMAT: protein microarray analysis tool. | 2006 | en-source [java] and r cod | |
| 16595561 | r | ProMAT: protein microarray analysis tool. | 2006 | urce java [and R] code. | |
| 16595560 | r | Pvclust: an R package for assessing the uncertainty in hierarchical clustering. | 2006 | clust: an [R package] for asses | |
| 16594991 | c++ | Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. | 2006 | a set of [C++] libraries | |
| 16574698 | r | SScore: an R package for detecting differential gene expression without gene expression summaries. | 2006 | score: an [R package] for detec | |
| 16574696 | mathlab | SBMLToolbox: an SBML toolbox for MATLAB users. | 2006 | olbox for [matlab] users. | |
| 16569235 | java | The Gaggle: an open-source software system for integrating bioinformatics software and data sources. | 2006 | en-source [java] software | |
| 16556315 | java | BioWarehouse: a bioinformatics database warehouse toolkit. | 2006 | the c and [java] languages | |
| 16551664 | java | BicAT: a biclustering analysis toolbox. | 2006 | tems. the [java] source co | |
| 16551355 | mathlab | Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. | 2006 | on of the [matlab] implement | |
| 16542435 | java | Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. | 2006 | ritten in [java] and is pu | |
| 16539707 | mathlab | mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. | 2006 | r-defined [matlab] code. | |
| 16526950 | r | An unsupervised classification scheme for improving predictions of prokaryotic TIS. | 2006 | udomallei [and R]. solanace | |
| 16522668 | java | MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data. | 2006 | cgt) is a [java] applicati | |
| 16522212 | java | MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. | 2006 | ) or as a [java] graphical | |
| 16522212 | perl | MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. | 2006 | tabase, a [perl] pipeline, | |
| 16519817 | java | VANTED: a system for advanced data analysis and visualization in the context of biological networks. | 2006 | nted as a [java] web start | |
| 16510496 | r | GALGO: an R package for multivariate variable selection using genetic algorithms. | 2006 | galgo: an [R package] for multi | |
| 16507094 | java | The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. | 2006 | a sample [java] client to | |
| 16504125 | mathlab | Multiscale Hy3S: hybrid stochastic simulation for supercomputers. | 2006 | ritten in [matlab], to help | |
| 16492684 | r | Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. | 2006 | programs [written in R] to do the | |
| 16473875 | perl | Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. | 2006 | ritten in [perl] using ope | |
| 16473874 | r | A new summarization method for Affymetrix probe level data. | 2006 | the farms [R package] is availa | |
| 16469097 | java | HotSwap for bioinformatics: a STRAP tutorial. | 2006 | using the [java] hotswap t | |
| 16466584 | java | JLIN: a java based linkage disequilibrium plotter. | 2006 | jlin: a [java] based lin | |
| 16466568 | java | BAMarraytrade mark: Java software for Bayesian analysis of variance for microarray data. | 2006 | ade mark: [java] software | |
| 16464251 | java | PathSys: integrating molecular interaction graphs for systems biology. | 2006 | able as a [java] web start | |
| 16455752 | r | affylmGUI: a graphical user interface for linear modeling of single channel microarray data. | 2006 | gui is an [R package] freely av | |
| 16452111 | perl | MAMMOT--a set of tools for the design, management and visualization of genomic tiling arrays. | 2006 | ection of [perl] and php s | |
| 16441875 | perl | Querying the public databases for sequences using complex keywords contained in the feature lines. | 2006 | specific [perl] scripts t | |
| 16434446 | java | ProteomeCommons.org JAF: reference information and tools for proteomics. | 2006 | nces. the [java] analysis | |
| 16418234 | java | Panta rhei (QAlign2): an open graphical environment for sequence analysis. | 2006 | s and the [java] source co | |
| 16410320 | r | Comparison of Affymetrix GeneChip expression measures. | 2006 | rt of the [Bioconductor] project ( | |
| 16410318 | java | Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting. | 2006 | the [java] classes a | |
| 16403793 | mathlab | Using a state-space model with hidden variables to infer transcription factor activities. | 2006 | data and [matlab] code will | |
| 16403221 | python | A high level interface to SCOP and ASTRAL implemented in python. | 2006 | mented in [python]. | |
| 16398931 | perl | Application of machine learning in SNP discovery. | 2006 | ritten in [perl] and can b | |
| 16397008 | perl | ANDY: a general, fault-tolerant tool for database searching on computer clusters. | 2006 | a set of [perl] programs | |
| 16377613 | java | Improving missing value estimation in microarray data with gene ontology. | 2006 | [java] and matla | |
| 16377613 | mathlab | Improving missing value estimation in microarray data with gene ontology. | 2006 | java and [matlab] codes are | |
| 16377612 | python | GenomeDiagram: a python package for the visualization of large-scale genomic data. | 2006 | iagram: a [python] package f | |
| 16371165 | r | WebArray: an online platform for microarray data analysis. | 2005 | ckages in [Bioconductor], need sop | |
| 16371163 | perl | The Gene Set Builder: collation, curation, and distribution of sets of genes. | 2005 | eatures a [perl] api (appl | |
| 16368771 | java | FLOSS: flexible ordered subset analysis for linkage mapping of complex traits. | 2006 | ritten in [java] for easy | |
| 16357032 | java | SEAN: SNP prediction and display program utilizing EST sequence clusters. | 2006 | iction. a [java] viewer is | |
| 16357031 | java | eQTL Explorer: integrated mining of combined genetic linkage and expression experiments. | 2006 | ata via a [java] graphical | |
| 16351742 | perl | ESTree db: a tool for peach functional genomics. | 2005 | developed [perl] scripts a | |
| 16332714 | perl | TRAP: automated classification, quantification and annotation of tandemly repeated sequences. | 2006 | ram, is a [perl] program t | |
| 16332708 | r | Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data. | 2006 | ent a new [R package] for the a | |
| 16332707 | python | BALLView: a tool for research and education in molecular modeling. | 2006 | language [python] it is eas | |
| 16332704 | java | PubMed Assistant: a biologist-friendly interface for enhanced PubMed search. | 2006 | veloped a [java] program, | |
| 16322049 | r | apTreeshape: statistical analysis of phylogenetic tree shape. | 2006 | hape is a [R package] dedicated | |
| 16321157 | r | ArrayQuest: a web resource for the analysis of DNA microarray data. | 2005 | as those [written in R], bioperl | |
| 16321157 | perl | ArrayQuest: a web resource for the analysis of DNA microarray data. | 2005 | ten in r, [bioperl] and c++; | |
| 16317076 | mathlab | Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. | 2006 | software [matlab]. the tool | |
| 16303798 | fortran | Statistical estimation of gene expression using multiple laser scans of microarrays. | 2006 | [fortran] 90 code f | |
| 16293669 | java | Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series. | 2006 | the [java] program, | |
| 16287941 | c++ | WindowMasker: window-based masker for sequenced genomes. | 2006 | the ncbi [C++] toolkit. | |
| 16287938 | mathlab | Classification of microarray data with factor mixture models. | 2006 | ritten in [matlab] and avail | |
| 16287932 | python | An efficient randomized algorithm for contact-based NMR backbone resonance assignment. | 2006 | dependent [python] code. the | |
| 16269418 | r | ClaNC: point-and-click software for classifying microarrays to nearest centroids. | 2006 | ble as an [R package]. | |
| 16269415 | java | LogoBar: bar graph visualization of protein logos with gaps. | 2006 | obar is a [java] applicati | |
| 16269077 | java | maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. | 2005 | chema and [java] applicati | |
| 16257986 | mathlab | Classification using functional data analysis for temporal gene expression data. | 2006 | [matlab] programs | |
| 16257984 | mathlab | Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. | 2006 | [matlab] source co | |
| 16249260 | mathlab | Gene selection using support vector machines with non-convex penalty. | 2006 | [matlab] codes are | |
| 16249259 | mathlab | Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. | 2006 | [matlab] source co | |
| 16239306 | python | ConFind: a robust tool for conserved sequence identification. | 2005 | requires [python] 2.3, but | |
| 16234319 | java | A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. | 2006 | nted as a [java] applet at | |
| 16216830 | r | The influence of missing value imputation on detection of differentially expressed genes from microarray data. | 2005 | the [R package] for linim | |
| 16204346 | r | Sample size determination for the false discovery rate. | 2005 | ed s-plus [and R] code libr | |
| 16204111 | c++ | RNA secondary structural alignment with conditional random fields. | 2005 | mented in [C++] is availa | |
| 16204098 | java | Recovering haplotype structure through recombination and gene conversion. | 2005 | mented in [java] and are a | |
| 16204097 | mathlab | Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. | 2005 | nted in a [matlab] package t | |
| 16204095 | c++ | A gamma mixture model better accounts for among site rate heterogeneity. | 2005 | [C++] source co | |
| 16188927 | r | HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients. | 2005 | ble as an [R package] and can b | |
| 16188923 | java | Medusa: a simple tool for interaction graph analysis. | 2005 | dusa is a [java] applicati | |
| 16188037 | c++ | SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. | 2005 | nted in a [C++] program n | |
| 16179358 | java | Doelan: a solution for quality control monitoring of microarray production. | 2005 | ritten in [java] and works | |
| 16166098 | mathlab | RSIR: regularized sliced inverse regression for motif discovery. | 2005 | [matlab] programs | |
| 16159919 | mathlab | Analysis of mass spectral serum profiles for biomarker selection. | 2005 | [matlab] scripts t | |
| 16159913 | r | A comparison study: applying segmentation to array CGH data for downstream analyses. | 2005 | ttp://www.[Bioconductor].org | |
| 16144805 | mathlab | Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences. | 2005 | mented in [matlab] code, and | |
| 16144548 | java | Generalizations of Markov model to characterize biological sequences. | 2005 | mented in [java] and is av | |
| 16141249 | java | BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. | 2005 | ed in the [java] programmi | |
| 16141248 | r | Network constrained clustering for gene microarray data. | 2005 | ted in an [R package] genent | |
| 16122395 | r | stam--a Bioconductor compliant R package for structured analysis of microarray data. | 2005 | compliant [R package] for struc | |
| 16118262 | mathlab | DNA microarray data imputation and significance analysis of differential expression. | 2005 | [matlab] code is a | |
| 16118259 | java | Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem. | 2005 | ritten in [java] is availa | |
| 16109746 | mathlab | A statistical model providing comprehensive predictions for the mRNA differential display. | 2005 | mented in [matlab] (the math | |
| 16105898 | java | MESHI: a new library of Java classes for molecular modeling. | 2005 | ibrary of [java] classes f | |
| 16102175 | r | Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. | 2005 | rt of the [Bioconductor] package m | |
| 16096348 | r | ROCR: visualizing classifier performance in R. | 2005 | atistical [language r]. it featu | |
| 16082012 | r | BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. | 2005 | is a new [Bioconductor] package t | |
| 16081474 | java | Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. | 2005 | lable via [java] web start | |
| 16076888 | r | Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. | 2005 | leaffy: a [Bioconductor] package f | |
| 16076886 | java | An automated genotyping system for analysis of HIV-1 and other microbial sequences. | 2005 | ped using [java] programmi | |
| 16076886 | perl | An automated genotyping system for analysis of HIV-1 and other microbial sequences. | 2005 | mming and [perl] scripts, | |
| 16051675 | java | SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. | 2005 | rams in a [java] applet an | |
| 16046497 | mathlab | Automated Microarray Image Analysis Toolbox for MATLAB. | 2005 | olbox for [matlab]. | |
| 16045803 | r | Evaluation of normalization methods for cDNA microarray data by k-NN classification. | 2005 | using the [R language] for stati | |
| 16042799 | perl | CGH-Profiler: data mining based on genomic aberration profiles. | 2005 | d through [perl] scripts.c | |
| 16030074 | perl | HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. | 2005 | a set of [perl] scripts a | |
| 16022740 | perl | Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi. | 2005 | a [perl] script pa | |
| 16020473 | java | MAVisto: a tool for the exploration of network motifs. | 2005 | arge as a [java] webstart | |
| 16020470 | r | A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips. | 2005 | ted in an [R package], which is | |
| 16020468 | r | goCluster integrates statistical analysis and functional interpretation of microarray expression data. | 2005 | e via the [Bioconductor] portal at | |
| 16011807 | r | Normal uniform mixture differential gene expression detection for cDNA microarrays. | 2005 | case. an [R package] called nu | |
| 16011796 | java | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. | 2005 | veloped a [java] tool, cal | |
| 16002431 | c++ | Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. | 2005 | also as a [C++] program i | |
| 15998662 | r | Local modeling of global interactome networks. | 2005 | nd in the [R package] apcomplex | |
| 15994196 | perl | SynBrowse: a synteny browser for comparative sequence analysis. | 2005 | en source [bioperl] modules. | |
| 15994194 | java | TO-GO: a Java-based Gene Ontology navigation environment. | 2005 | nted as a [java] applicati | |
| 15992409 | perl | Prediction of twin-arginine signal peptides. | 2005 | based on [perl] syntax re | |
| 15987530 | r | Species-specific analysis of protein sequence motifs using mutual information. | 2005 | sing perl [and R] as well a | |
| 15987530 | perl | Species-specific analysis of protein sequence motifs using mutual information. | 2005 | ice using [perl] and r as | |
| 15985178 | python | Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. | 2005 | f fccd in [python] is availa | |
| 15976072 | java | ACT: the Artemis Comparison Tool. | 2005 | ritten in [java] and can r | |
| 15972284 | java | BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. | 2005 | en-source [java] tool to d | |
| 15969769 | perl | transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. | 2005 | en-source [perl] script th | |
| 15961495 | mathlab | Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data. | 2005 | mented in [matlab], r and ne | |
| 15961487 | r | Robust classification modeling on microarray data using misclassification penalized posterior. | 2005 | le at the [Bioconductor] website ( | |
| 15961469 | perl | A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. | 2005 | s in r or [perl] are avail | |
| 15961466 | java | High-recall protein entity recognition using a dictionary. | 2005 | mented in [java]. algorith | |
| 15961453 | java | Clustering short time series gene expression data. | 2005 | taining a [java] implement | |
| 15961441 | java | caBIONet--A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases. | 2005 | veloped a [java] based dat | |
| 15961440 | java | Querying and computing with BioCyc databases. | 2005 | perl and [java], and sql | |
| 15961440 | perl | Querying and computing with BioCyc databases. | 2005 | for lisp, [perl] and java, | |
| 15960857 | perl | AutoFACT: an automatic functional annotation and classification tool. | 2005 | mented in [perl] and runs | |
| 15947019 | perl | A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm. | 2005 | eloped in [perl] (v. 5.8, | |
| 15947017 | python | Sarment: Python modules for HMM analysis and partitioning of sequences. | 2005 | sarment: [python] modules f | |
| 15941744 | r | Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'. | 2005 | , j. shih [and R]. simon on | |
| 15938750 | c++ | libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. | 2005 | libcov: a [C++] bioinform | |
| 15932904 | c++ | Statistics of protein library construction. | 2005 | rface and [C++] source co | |
| 15932902 | python | PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes. | 2005 | a set of [python] scripts t | |
| 15910684 | c | Genome comparison without alignment using shortest unique substrings. | 2005 | hulen are [written in C] and avail | |
| 15905279 | mathlab | Semi-supervised protein classification using cluster kernels. | 2005 | he spider [matlab] package i | |
| 15905277 | r | Prediction error estimation: a comparison of resampling methods. | 2005 | f results [and R] code for | |
| 15905276 | java | CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. | 2005 | the free [java] runtime e | |
| 15905274 | java | Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. | 2005 | using the [java] language | |
| 15905273 | java | Dasty and UniProt DAS: a perfect pair for protein feature visualization. | 2005 | ted using [java] and macro | |
| 15879451 | perl | Fast parsers for Entrez Gene. | 2005 | larity of [perl] programmi | |
| 15860559 | java | ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. | 2005 | ncludes a [java] applicati | |
| 15855247 | java | jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. | 2005 | ydit is a [java] applicati | |
| 15845656 | r | Donuts, scratches and blanks: robust model-based segmentation of microarray images. | 2005 | ntributed [R package] mclust fo | |
| 15840706 | perl | SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. | 2005 | link is a [perl] script th | |
| 15836795 | java | MARS: microarray analysis, retrieval, and storage system. | 2005 | he latest [j2ee] applicati | |
| 15829007 | r | ProGenExpress: visualization of quantitative data on prokaryotic genomes. | 2005 | press, an [R package] that allo | |
| 15827079 | perl | Visualizing profile-profile alignment: pairwise HMM logos. | 2005 | ownload a [perl] package t | |
| 15817693 | python | Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. | 2005 | and-alone [python] program t | |
| 15817692 | c++ | Stochastic reaction-diffusion simulation with MesoRD. | 2005 | ritten in [C++] and licen | |
| 15817688 | r | twilight; a Bioconductor package for estimating the local false discovery rate. | 2005 | ilight; a [Bioconductor] package f | |
| 15817687 | c++ | pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. | 2005 | with the [C++] stl, .net | |
| 15814553 | c++ | BEST: binding-site estimation suite of tools. | 2005 | in qt, a [C++] applicati | |
| 15807904 | java | CGHPRO -- a comprehensive data analysis tool for array CGH. | 2005 | and-alone [java] applicati | |
| 15804359 | c++ | Super paramagnetic clustering of protein sequences. | 2005 | use using [C++] and it is | |
| 15802285 | fortran | Density guided importance sampling: application to a reduced model of protein folding. | 2005 | [fortran] code avai | |
| 15797915 | r | MADE4: an R package for multivariate analysis of gene expression data. | 2005 | made4: an [R package] for multi | |
| 15788106 | perl | Wildfire: distributed, Grid-enabled workflow construction and execution. | 2005 | e such as [perl]. programm | |
| 15780146 | mathlab | MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. | 2005 | oolbox: a [matlab] toolbox f | |
| 15769840 | java | SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). | 2005 | mented by [java] and perl. | |
| 15769840 | perl | SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). | 2005 | java and [perl]. snpnb ca | |
| 15757508 | java | JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases. | 2005 | asview: a [java] atlas-vie | |
| 15746275 | java | Partition-distance via the assignment problem. | 2005 | ritten in [java] is availa | |
| 15723693 | java | Atlas - a data warehouse for integrative bioinformatics. | 2005 | ges: c++, [java], and perl | |
| 15723693 | c++ | Atlas - a data warehouse for integrative bioinformatics. | 2005 | anguages: [C++], java, an | |
| 15723693 | perl | Atlas - a data warehouse for integrative bioinformatics. | 2005 | java, and [perl]. the meth | |
| 15713734 | fortran | FastContact: rapid estimate of contact and binding free energies. | 2005 | ritten in [fortran]. the exec | |
| 15705654 | r | Estimating cancer survival and clinical outcome based on genetic tumor progression scores. | 2005 | datasets [and R] code for | |
| 15699024 | fortran | Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method. | 2005 | ion.html. [fortran] 90 code a | |
| 15694009 | java | The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. | 2005 | ritten in [java], thus off | |
| 15677704 | r | Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. | 2005 | compliant [R package] | |
| 15673564 | r | Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. | 2005 | his paper [and R] code for | |
| 15673564 | mathlab | Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. | 2005 | [matlab] scripts t | |
| 15671116 | mathlab | Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. | 2005 | e form of [matlab] script fi | |
| 15671115 | perl | TruMatch--a BLAST post-processor that identifies bona fide sequence matches to genome assemblies. | 2005 | ritten in [perl] and is fr | |
| 15657105 | r | Testing association of a pathway with survival using gene expression data. | 2005 | ttp://www.[Bioconductor].org | |
| 15657102 | r | Use of within-array replicate spots for assessing differential expression in microarray experiments. | 2005 | from the [CRAN] repositor | |
| 15647304 | java | AGML Central: web based gel proteomic infrastructure. | 2005 | tering. a [java] applet vi | |
| 15647300 | java | Detecting clusters of different geometrical shapes in microarray gene expression data. | 2005 | ped using [java] language, | |
| 15647291 | perl | ALOHOMORA: a tool for linkage analysis using 10K SNP array data. | 2005 | ritten in [perl] and may b | |
| 15642112 | java | Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. | 2005 | used the [java] data obje | |
| 15634352 | perl | Visualization of comparative genomic analyses by BLAST score ratio. | 2005 | nted in a [perl] script, c | |
| 15613388 | java | An enhanced Java graph applet interface for visualizing interactomes. | 2005 | enhanced [java] graph app | |
| 15598833 | r | Differential gene expression detection using penalized linear regression models: the improved SAM statistics. | 2005 | s results [and R] functions | |
| 15598829 | c++ | CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping. | 2005 | used as a [C++] library, | |
| 15593402 | mathlab | CGH-Plotter: MATLAB toolbox for CGH-data analysis. | 2003 | -plotter: [matlab] toolbox f | |
| 15593401 | java | GFPE: gene-finding program evaluation. | 2003 | a set of [java] classes f | |
| 15588288 | java | ABC: software for interactive browsing of genomic multiple sequence alignment data. | 2004 | teractive [java] software | |
| 15585532 | perl | TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences. | 2005 | a set of [perl] scripts t | |
| 15585529 | java | RBT--a tool for building refined Buneman trees. | 2005 | ritten in [java], is avail | |
| 15585527 | r | OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. | 2005 | available [R package]. addition | |
| 15585059 | r | A two-way interface between limited Systems Biology Markup Language and R. | 2004 | language [and R]. | |
| 15572472 | java | Generalized Venn diagrams: a new method of visualizing complex genetic set relations. | 2005 | teractive [java] applicati | |
| 15550481 | java | CRAVE: a database, middleware and visualization system for phenotype ontologies. | 2005 | ccessible [java] applicati | |
| 15546938 | c++ | PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. | 2005 | ms-visual [C++], has a cl | |
| 15541170 | r | Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. | 2004 | -platform [R package] aroma, wh | |
| 15531616 | perl | ESTminer: a suite of programs for gene and allele identification. | 2005 | ritten in [perl] and are f | |
| 15531613 | mathlab | The SBW-MATLAB interface. | 2005 | ce allows [matlab] users to | |
| 15531604 | java | A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns. | 2005 | a [java] tool for | |
| 15509605 | r | Implementation of a gene expression index calculation method based on the PDNN model. | 2005 | atistical [language r]. | |
| 15509599 | java | MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations. | 2005 | veloped a [java] package, | |
| 15488149 | java | Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. | 2004 | en source [java] applicati | |
| 15479716 | java | Circular genome visualization and exploration using CGView. | 2005 | wer) is a [java] applicati | |
| 15477491 | c++ | GenomeMixer: a complex genetic cross simulator. | 2004 | entation, [C++] source, a | |
| 15466910 | r | BagBoosting for tumor classification with gene expression data. | 2004 | ble as an [R package] under gnu | |
| 15458579 | perl | GeneXplorer: an interactive web application for microarray data visualization and analysis. | 2004 | load from [CPAN] http://se | |
| 15458579 | javascript | GeneXplorer: an interactive web application for microarray data visualization and analysis. | 2004 | html and [javascript] to displa | |
| 15454413 | r | arrayMagic: two-colour cDNA microarray quality control and preprocessing. | 2005 | the [R package] arraymagi | |
| 15454409 | python | Modelling cellular systems with PySCeS. | 2005 | the [python] simulator | |
| 15381628 | r | Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. | 2004 | the [R package] glad (gai | |
| 15377505 | perl | HaploPainter: a tool for drawing pedigrees with complex haplotypes. | 2005 | ritten in [perl] and may b | |
| 15374874 | c | Clann: investigating phylogenetic information through supertree analyses. | 2005 | en in the [C programming] language. | |
| 15374872 | r | An experimental evaluation of a loop versus a reference design for two-channel microarrays. | 2005 | the data [and R] code are | |
| 15374871 | r | VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data. | 2005 | the [R package] is freely | |
| 15374867 | mathlab | Improving genome annotations using phylogenetic profile anomaly detection. | 2005 | ted using [matlab] and open | |
| 15374864 | java | ESTminer: a Web interface for mining EST contig and cluster databases. | 2005 | mented in [java] and the | |
| 15374860 | mathlab | Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods. | 2005 | rms where [matlab] is availa | |
| 15374858 | java | Expression-based monitoring of transcription factor activity: the TELiS database. | 2005 | erlocking [java] applicati | |
| 15355552 | mathlab | Iterative class discovery and feature selection using Minimal Spanning Trees. | 2004 | ions. the [matlab] programs | |
| 15353451 | mathlab | A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. | 2005 | x.htm and [matlab] source co | |
| 15353448 | java | SNAP: workbench management tool for evolutionary population genetic analysis. | 2005 | kbench, a [java] program t | |
| 15347576 | perl | easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses. | 2005 | inkage: a [perl] script fo | |
| 15339346 | c++ | Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data. | 2004 | easures.a [C++] source co | |
| 15339345 | r | Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). | 2004 | ool or as [R language] scripts a | |
| 15333457 | java | OntologyTraverser: an R package for GO analysis. | 2005 | stem uses [java] to instan | |
| 15333457 | r | OntologyTraverser: an R package for GO analysis. | 2005 | erser: an [R package] for go an | |
| 15319258 | java | Simulating genetic networks made easy: network construction with simple building blocks. | 2005 | the [java] program, | |
| 15310559 | python | BlastAlign: a program that uses blast to align problematic nucleotide sequences. | 2005 | perl and [python] and will | |
| 15310559 | perl | BlastAlign: a program that uses blast to align problematic nucleotide sequences. | 2005 | s of both [perl] and pytho | |
| 15308543 | java | SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data. | 2005 | hart is a [java] applicati | |
| 15297302 | java | Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. | 2004 | her via a [java] user inte | |
| 15297301 | r | Network structures and algorithms in Bioconductor. | 2005 | rithms in [Bioconductor]. | |
| 15297299 | perl | GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. | 2004 | -oriented [perl] modules f | |
| 15297296 | r | limmaGUI: a graphical user interface for linear modeling of microarray data. | 2004 | ted as an [R package]. the soft | |
| 15284097 | java | CLANS: a Java application for visualizing protein families based on pairwise similarity. | 2004 | clans: a [java] applicati | |
| 15271780 | mathlab | A probabilistic measure for alignment-free sequence comparison. | 2004 | ritten in [matlab] are avail | |
| 15271779 | java | Data exploration tools for the Gene Ontology database. | 2004 | based on [java] 2 enterpr | |
| 15271778 | mathlab | Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. | 2004 | e a novel [matlab] toolbox f | |
| 15262800 | c | An efficient algorithm for detecting frequent subgraphs in biological networks. | 2004 | ms in the [C programming] language | |
| 15262781 | c++ | Analysis of domain correlations in yeast protein complexes. | 2004 | the ncbi [C++] toolkit. | |
| 15262778 | r | Statistical modeling of sequencing errors in SAGE libraries. | 2004 | ted as an [R package]. an onlin | |
| 15262777 | mathlab | Deconvolving cell cycle expression data with complementary information. | 2004 | [matlab] implement | |
| 15256416 | r | Importing MAGE-ML format microarray data into BioConductor. | 2004 | data into [Bioconductor]. | |
| 15256415 | r | A graph-theoretic approach to testing associations between disparate sources of functional genomics data. | 2004 | ttp://www.[Bioconductor].org. | |
| 15256401 | perl | CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. | 2004 | tem, csh, [perl] and mysql | |
| 15253776 | java | Base-By-Base: single nucleotide-level analysis of whole viral genome alignments. | 2004 | net using [java] web start | |
| 15247095 | java | VisRD--visual recombination detection. | 2004 | ritten in [java] and is de | |
| 15230973 | perl | mlstdbNet - distributed multi-locus sequence typing (MLST) databases. | 2004 | rsed by a [perl] cgi scrip | |
| 15201188 | java | The CRASSS plug-in for integrating annotation data with hierarchical clustering results. | 2004 | nted as a [java] plug-in f | |
| 15201186 | java | SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays. | 2004 | mented in [java], which si | |
| 15201182 | c++ | Breakpoint identification and smoothing of array comparative genomic hybridization data. | 2004 | in visual [C++], has a us | |
| 15189572 | mathlab | M-CGH: analysing microarray-based CGH experiments. | 2004 | -cgh is a [matlab] toolbox w | |
| 15180939 | java | A statistical framework for the design of microarray experiments and effective detection of differential gene expression. | 2004 | nted as a [java] applicati | |
| 15180930 | java | Java Treeview--extensible visualization of microarray data. | 2004 | [java] treeview- | |
| 15176974 | perl | Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. | 2004 | equently, [perl] software | |
| 15166027 | r | Regulatory motif finding by logic regression. | 2004 | d.html an [R package] for mfure | |
| 15145813 | java | ClutrFree: cluster tree visualization and interpretation. | 2004 | clutrfree [java] source co | |
| 15117754 | mathlab | Identification of DNA regulatory motifs using Bayesian variable selection. | 2004 | the [matlab] code for | |
| 15117748 | java | YAdumper: extracting and translating large information volumes from relational databases to structured flat files. | 2004 | mper is a [java] applicati | |
| 15113410 | java | A web services choreography scenario for interoperating bioinformatics applications. | 2004 | ard coded [java] applicati | |
| 15105279 | java | GDPC: connecting researchers with multiple integrated data sources. | 2004 | ritten in [java] and provi | |
| 15105278 | java | ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences. | 2004 | suite of [java] programs | |
| 15087316 | java | Sfixem--graphical sequence feature display in Java. | 2004 | isplay in [java]. | |
| 15087313 | mathlab | Analysis of longitudinal metabolomics data. | 2004 | files for [matlab] for the a | |
| 15087311 | fortran | MathSBML: a package for manipulating SBML-based biological models. | 2004 | html and [fortran]. by acces | |
| 15073026 | java | ArrayNorm: comprehensive normalization and analysis of microarray data. | 2004 | dependent [java] applicati | |
| 15073025 | java | Pedro: a configurable data entry tool for XML. | 2004 | edro is a [java] applicati | |
| 15073017 | perl | Alignment of RNA base pairing probability matrices. | 2004 | mented in [perl] and can b | |
| 15072998 | java | Web-based kinetic modelling using JWS Online. | 2004 | ser based [java] applets, | |
| 15059840 | java | MuSiC: a tool for multiple sequence alignment with constraints. | 2004 | mented in [java] language | |
| 15059837 | mathlab | Extraction of fluorescent cell puncta by adaptive fuzzy segmentation. | 2004 | ritten in [matlab] are avail | |
| 15059834 | java | Designing and executing scientific workflows with a programmable integrator. | 2004 | irements: [java] v1.3 (htt | |
| 15059827 | perl | SCANMS: adjusting for multiple comparisons in sliding window neutrality tests. | 2004 | a [perl] utility c | |
| 15059823 | c++ | PedSplit: pedigree management for stratified analysis. | 2004 | cutables, [C++] source co | |
| 15059819 | java | Pelican: pedigree editor for linkage computer analysis. | 2004 | igher). a [java] web start | |
| 15044243 | mathlab | Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. | 2004 | [matlab] code and | |
| 15044236 | java | ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. | 2004 | nted as a [java] applet. | |
| 15040818 | perl | The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. | 2004 | formative [perl] script. t | |
| 15033875 | r | Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes. | 2004 | rg or www.[Bioconductor].org | |
| 15033871 | perl | Optimization models for cancer classification: extracting gene interaction information from microarray expression data. | 2004 | do.com. a [perl] script th | |
| 15033870 | java | Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. | 2004 | wser with [java] plug-in 1 | |
| 15033868 | r | Enhancing scatterplots with smoothed densities. | 2004 | or matlab [and R] are avail | |
| 15033868 | mathlab | Enhancing scatterplots with smoothed densities. | 2004 | tions for [matlab] and r are | |
| 14988125 | mathlab | Decoupling dynamical systems for pathway identification from metabolic profiles. | 2004 | with the [matlab] module bs | |
| 14988124 | r | Mixture models for assessing differential expression in complex tissues using microarray data. | 2004 | ds in the [R language] can be do | |
| 14988123 | java | GeneCluster 2.0: an advanced toolset for bioarray analysis. | 2004 | and-alone [java] applicati | |
| 14988118 | r | matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. | 2004 | the [R package] matchprob | |
| 14988110 | mathlab | Robust PCA and classification in biosciences. | 2004 | rt of the [matlab] toolbox f | |
| 14988107 | java | TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. | 2004 | is a new [java] graphical | |
| 14988100 | java | Haplotypes histories as pathways of recombinations. | 2004 | oped on a [java] platform | |
| 14962941 | java | ToPNet--an application for interactive analysis of expression data and biological networks. | 2004 | is a pure [java] applicati | |
| 14962938 | mathlab | Modeling T-cell activation using gene expression profiling and state-space models. | 2004 | data and [matlab] computer | |
| 14962926 | c++ | A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. | 2004 | mented in [C++] in a prog | |
| 14962918 | python | Amplicon: software for designing PCR primers on aligned DNA sequences. | 2004 | form with [python] 2.3 insta | |
| 14962913 | perl | Simple sequence repeat marker loci discovery using SSR primer. | 2004 | ritten in [perl] and is fr | |
| 14960475 | perl | VisCoSe: visualization and comparison of consensus sequences. | 2004 | mand line [perl] script fo | |
| 14960472 | java | The Jalview Java alignment editor. | 2004 | e jalview [java] alignment | |
| 14960468 | c++ | LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. | 2004 | mented in [C++] that allo | |
| 14960468 | perl | LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. | 2004 | lddist: a [perl] module fo | |
| 14960456 | r | affy--analysis of Affymetrix GeneChip data at the probe level. | 2004 | age is an [R package] of functi | |
| 14871871 | c++ | Bayesian mixture model based clustering of replicated microarray data. | 2004 | esponding [C++] code are | |
| 14871861 | python | Open source clustering software. | 2004 | nerated a [python] and a per | |
| 14871861 | c++ | Open source clustering software. | 2004 | her c and [C++] programs. | |
| 14871861 | perl | Open source clustering software. | 2004 | hon and a [perl] interface | |
| 14871859 | java | CNplot: visualizing pre-clustered networks. | 2004 | a [java] implement | |
| 14764576 | java | Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology. | 2004 | xml-based [java] applicati | |
| 14764570 | java | GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. | 2004 | . it uses [java] applet-se | |
| 14764568 | perl | Sequence analysis and membrane partitioning energies of alpha-helical antimicrobial peptides. | 2004 | zed using [perl] programs. | |
| 14764558 | java | An evaluation of new criteria for CpG islands in the human genome as gene markers. | 2004 | cpgie, a [java] software | |
| 14764554 | c | Multiple sequence alignment in parallel on a workstation cluster. | 2004 | kstations [using C] and messa | |
| 14764551 | r | ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics. | 2004 | viz is an [R package] for the v | |
| 14751995 | perl | Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. | 2004 | atlab and [perl] code used | |
| 14751995 | mathlab | Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. | 2004 | the [matlab] and perl | |
| 14751994 | mathlab | Predicting protein structure classes from function predictions. | 2004 | [matlab] code is a | |
| 14751988 | java | Java-based application framework for visualization of gene regulatory region annotations. | 2004 | es, using [java] technolog | |
| 14751975 | java | Visualization of near-optimal sequence alignments. | 2004 | sent to a [java] applet, w | |
| 14751975 | c++ | Visualization of near-optimal sequence alignments. | 2004 | face to a [C++] program g | |
| 14734327 | r | APE: Analyses of Phylogenetics and Evolution in R language. | 2004 | official [R package] archive a | |
| 14734323 | java | JDotter: a Java interface to multiple dotplots generated by dotter. | 2004 | dotter: a [java] interface | |
| 14734312 | mathlab | Comparative evaluation of word composition distances for the recognition of SCOP relationships. | 2004 | all [matlab] code used | |
| 14734308 | python | A comparative phylogenetic approach for dating whole genome duplication events. | 2004 | en in the [python] programmi | |
| 14734306 | perl | Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. | 2004 | [perl] program a | |
| 14734305 | perl | Transposable element annotation of the rice genome. | 2004 | a set of [perl] scripts. | |
| 14715091 | perl | Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. | 2004 | in c and [perl]. the code | |
| 14706121 | python | PyEvolve: a toolkit for statistical modelling of molecular evolution. | 2004 | standard [python] code to d | |
| 14693822 | java | BugView: a browser for comparing genomes. | 2004 | view is a [java] applicati | |
| 14693819 | c++ | GRIL: genome rearrangement and inversion locator. | 2004 | mented in [C++] and runs | |
| 14693816 | mathlab | Adjustment of systematic microarray data biases. | 2004 | [matlab] software | |
| 14693814 | r | A global test for groups of genes: testing association with a clinical outcome. | 2004 | ttp://www.[Bioconductor].org | |
| 14693813 | java | VizStruct: exploratory visualization for gene expression profiling. | 2004 | ritten in [java] and matla | |
| 14693813 | mathlab | VizStruct: exploratory visualization for gene expression profiling. | 2004 | java and [matlab] and softw | |
| 14693803 | r | Identifying periodically expressed transcripts in microarray time series data. | 2004 | ed in the [R package] genets av | |
| 14678565 | java | AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis. | 2003 | ddleware, [java], jdbc, an | |
| 14668247 | perl | Characterizing gene sets with FuncAssociate. | 2003 | code (in [perl] and c) is | |
| 14668233 | r | A CART-based approach to discover emerging patterns in microarray data. | 2003 | atistical [language r] implement | |
| 14668224 | java | caCORE: a common infrastructure for cancer informatics. | 2003 | provides [java], simple o | |
| 14668219 | c | Efficient estimation of emission probabilities in profile hidden Markov models. | 2003 | lgorithms [written in C] language | |
| 14668218 | java | JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration. | 2003 | eralized, [java] xml-based | |
| 14630669 | c++ | NCL: a C++ class library for interpreting data files in NEXUS format. | 2003 | ncl: a [C++] class lib | |
| 14630667 | c++ | Libsequence: a C++ class library for evolutionary genetic analysis. | 2003 | quence: a [C++] class lib | |
| 14630665 | mathlab | Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. | 2003 | ritten in [matlab], and bina | |
| 14630660 | python | PDB file parser and structure class implemented in Python. | 2003 | mented in [python]. | |
| 14630649 | mathlab | MGraph: graphical models for microarray data analysis. | 2003 | roduces a [matlab] toolbox, | |
| 14604444 | java | PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. | 2003 | ritten in [java] that can | |
| 14594724 | java | RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events. | 2003 | ed-t is a [java] applicati | |
| 14594722 | java | LDA--a java-based linkage disequilibrium analyzer. | 2003 | user, the [jre] version 1 | |
| 14594719 | java | An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data. | 2003 | [java] software | |
| 14594459 | java | GeneViTo: visualizing gene-product functional and structural features in genomic datasets. | 2003 | propriate [java] runtime e | |
| 14583100 | java | A knowledge discovery object model API for Java. | 2003 | l api for [java]. | |
| 14555636 | java | GCHap: fast MLEs for haplotype frequencies by gene counting. | 2003 | the [java] classes a | |
| 14555628 | r | Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. | 2003 | th s-plus [and R] functions | |
| 14534191 | python | Finding optimal degenerate patterns in DNA sequences. | 2003 | the [python] script su | |
| 14512356 | java | The design of Jemboss: a graphical user interface to EMBOSS. | 2003 | ritten in [java] and is do | |
| 14512356 | c | The design of Jemboss: a graphical user interface to EMBOSS. | 2003 | en in the [C language]. another | |
| 14512353 | c | Transformation and normalization of oligonucleotide microarray data. | 2003 | a program [written in C] is availa | |
| 14512352 | java | Controlling false-negative errors in microarray differential expression analysis: a PRIM approach. | 2003 | estanding [java] applicati | |
| 12962546 | perl | Genome-wide prediction, display and refinement of binding sites with information theory-based models. | 2003 | cripts in [perl]. multi-pr | |
| 12875658 | java | Evolutionary algorithms for the selection of single nucleotide polymorphisms. | 2003 | spea2) in [java]. our impl | |
| 12874048 | mathlab | Exact significance levels for the maximum chi(2) method of detecting recombination. | 2003 | [matlab] source co | |
| 12874047 | mathlab | Estimation of transformation parameters for microarray data. | 2003 | r and [matlab] code and | |
| 12835278 | c | Calculation of helix packing angles in protein structures. | 2003 | [C language] source co | |
| 12835277 | perl | GeneComber: combining outputs of gene prediction programs for improved results. | 2003 | en in the [perl] programmi | |
| 12835276 | java | Longest biased interval and longest non-negative sum interval. | 2003 | [java] code of t | |
| 12835275 | java | TableView: portable genomic data visualization. | 2003 | ritten in [java], tablevie | |
| 12801871 | mathlab | Novel clustering algorithm for microarray expression data in a truncated SVD space. | 2003 | ilable as [matlab] programs | |
| 12801870 | r | Simultaneous gene clustering and subset selection for sample classification via MDL. | 2003 | ed in the [R language]. the sour | |
| 12801869 | r | Bagging to improve the accuracy of a clustering procedure. | 2003 | ttp://www.[Bioconductor].org. | |
| 12801867 | c++ | K-ary clustering with optimal leaf ordering for gene expression data. | 2003 | rithms in [C++] on the li | |
| 12761071 | java | Ligand-Info, searching for similar small compounds using index profiles. | 2003 | uires the [java] runtime e | |
| 12761070 | java | ACGT-a comparative genomics tool. | 2003 | ritten in [java] and can b | |
| 12761060 | mathlab | Fuzzy C-means method for clustering microarray data. | 2003 | text and [matlab] functions | |
| 12761052 | java | FPV: fast protein visualization using Java 3D. | 2003 | ion using [java] 3d. | |
| 12724301 | perl | GeneMerge--post-genomic analysis, data mining, and hypothesis testing. | 2003 | ritten in [perl] that retu | |
| 12724295 | java | ALES: cell lineage analysis and mapping of developmental events. | 2003 | compliant [java] 2 environ | |
| 12720549 | c++ | DNA microarray data and contextual analysis of correlation graphs. | 2003 | e data. a [C++] implement | |
| 12697067 | perl | Significance analysis of lexical bias in microarray data. | 2003 | ilable as [perl] source or | |
| 12691998 | java | GoFish finds genes with combinations of Gene Ontology attributes. | 2003 | fish is a [java] applicati | |
| 12691997 | java | Java editor for biological pathways. | 2003 | [java] editor fo | |
| 12691990 | java | Client-server environment for high-performance gene expression data analysis. | 2003 | scalable [java] environme | |
| 12651733 | java | PedNavigator: a pedigree drawing servlet for large and inbred populations. | 2003 | ritten in [java] and is in | |
| 12651728 | mathlab | MatArray: a Matlab toolbox for microarray data. | 2003 | tarray: a [matlab] toolbox f | |
| 12611807 | mathlab | Alignment-free sequence comparison-a review. | 2003 | mented in [matlab] code and | |
| 12611802 | mathlab | Clustering of time-course gene expression data using a mixed-effects model with B-splines. | 2003 | [matlab] programs | |
| 12611799 | mathlab | An information theoretic approach for analyzing temporal patterns of gene expression. | 2003 | nsi c and [matlab] (mathwork | |
| 12611798 | fortran | Can transcriptome size be estimated from SAGE catalogs? | 2003 | to share [fortran] sourcecod | |
| 12584141 | perl | Wrapping up BLAST and other applications for use on Unix clusters. | 2003 | eloped in [perl] on a 20-n | |
| 12584131 | perl | Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. | 2003 | ritten in [perl] and is fr | |
| 12538267 | python | ARIA: automated NOE assignment and NMR structure calculation. | 2003 | sspeaks), [python] scripts f | |
| 12538266 | c | DPX: for the analysis of the protein core. | 2003 | e program [written in C] and its s | |
| 12538262 | perl | G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. | 2003 | a set of [perl] libraries | |
| 12538259 | c | RnaViz 2: an improved representation of RNA secondary structure. | 2003 | ng pieces [written in C] and in th | |
| 12538256 | java | AVA: visual analysis of gene expression microarray data. | 2003 | zer) is a [java] program t | |
| 12538252 | c++ | An efficient algorithm for minimal primer set selection. | 2003 | mented in [C++] programmi | |
| 12538248 | mathlab | FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. | 2003 | ckage for [matlab] and facil | |
| 12538244 | perl | A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins. | 2003 | t for the [perl] program f | |
| 12538241 | python | Rank order metrics for quantifying the association of sequence features with gene regulation. | 2003 | a [python] program f | |
| 12538238 | r | A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. | 2003 | rt of the [R package] affy, whi | |
| 12538236 | mathlab | Chemometric modelling based on 2D-fluorescence spectra without a calibration measurement. | 2003 | the [mathlab] routine i | |
| 12513700 | java | SeqVISTA: a graphical tool for sequence feature visualization and comparison. | 2003 | em with a [java] 1.4 virtu | |
| 12511063 | python | Phase4: automatic evaluation of database search methods. | 2002 | language [python] whose obj | |
| 12499313 | javascript | ModView, visualization of multiple protein sequences and structures. | 2003 | d through [javascript] commands | |
| 12499308 | r | An extensible application for assembling annotation for genomic data. | 2003 | der is an [R package] for assem | |
| 12499304 | c++ | Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations. | 2003 | a [C++] library f | |
| 12493080 | java | ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files. | 2002 | a [java] program w | |
| 12424130 | java | Poxvirus Orthologous Clusters (POCs). | 2002 | ocs) is a [java] client-se | |
| 12424129 | perl | GeneCards 2002: towards a complete, object-oriented, human gene compendium. | 2002 | -oriented [perl], migratio | |
| 12401134 | c++ | SeqHound: biological sequence and structure database as a platform for bioinformatics research. | 2002 | erl, c or [C++] remote ap | |
| 12401134 | perl | SeqHound: biological sequence and structure database as a platform for bioinformatics research. | 2002 | through a [perl], c or c++ | |
| 12398795 | perl | Making sense of EST sequences by CLOBBing them. | 2002 | ed on the [perl] scripting | |
| 12385980 | c++ | Modeling splicing sites with pairwise correlations. | 2002 | the [C++] source co | |
| 12376386 | perl | Genquire: genome annotation browser/editor. | 2002 | existing [bioperl] data mode | |
| 12376379 | c++ | Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility. | 2002 | the [C++] source co | |
| 12376376 | mathlab | Gene perturbation and intervention in probabilistic Boolean networks. | 2002 | ritten in [matlab] for simul | |
| 12366869 | perl | Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region. | 2002 | suite of [perl] scripts t | |
| 12230038 | java | The Bio* toolkits--a brief overview. | 2002 | ython and [biojava] projects | |
| 12230038 | python | The Bio* toolkits--a brief overview. | 2002 | bioperl, [biopython] and bioja | |
| 12230038 | perl | The Bio* toolkits--a brief overview. | 2002 | en source [bioperl], biopytho | |
| 12217927 | java | An ontology driven architecture for derived representations of macromolecular structure. | 2002 | ader. the [java] source co | |
| 12217926 | java | Applications of Tree-Maps to hierarchical biological data. | 2002 | [java] class fil | |
| 12217919 | java | VIZARD: analysis of Affymetrix Arabidopsis GeneChip data. | 2002 | zard is a [java] program c | |
| 12176842 | perl | DiffTool: building, visualizing and querying protein clusters. | 2002 | . all the [perl] sources a | |
| 12176840 | mathlab | MArray: analysing single, replicated or reversed microarray experiments. | 2002 | rray is a [matlab] toolbox w | |
| 12176838 | perl | TFBS: Computational framework for transcription factor binding site analysis. | 2002 | -oriented [perl] modules f | |
| 12169562 | java | PseudoViewer: automatic visualization of RNA pseudoknots. | 2002 | nted in a [java] program, | |
| 12117796 | c | CX, an algorithm that identifies protruding atoms in proteins. | 2002 | e program [written in C] and its s | |
| 12075029 | java | BAOBAB: a Java editor for large phylogenetic trees. | 2002 | baobab: a [java] editor fo | |
| 12050079 | perl | A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis. | 2002 | ent (dbi) [perl] to annota | |
| 12050073 | java | Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. | 2002 | ritten in [java] and is fr | |
| 12028595 | java | RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. | 2002 | ral c and [java] programs. | |
| 12028595 | perl | RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. | 2002 | mented as [perl] pipeline | |
| 12019022 | perl | NBLAST: a cluster variant of BLAST for NxN comparisons. | 2002 | c/c++ and [perl] applicati | |
| 12016048 | java | Compensation for nucleotide bias in a genome by representation as a discrete channel with noise. | 2002 | ignal.' a [java] applicati | |
| 11934743 | java | PatternHunter: faster and more sensitive homology search. | 2002 | t support [java]. patternh | |
| 11847095 | javascript | The EBI SRS server--recent developments. | 2002 | icksearch [javascript] interface | |
| 11836236 | java | PCSB--a program collection for structural biology and biophysical chemistry. | 2002 | ackage of [java] classes s | |
| 11836235 | java | Genesis: cluster analysis of microarray data. | 2002 | sy to use [java] suite for | |
| 11836221 | java | The Binding Database: data management and interface design. | 2002 | cted with [java] servlet t | |
| 11836216 | java | Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. | 2002 | mented in [java] and calcu | |
| 11751242 | c | CONSEL: for assessing the confidence of phylogenetic tree selection. | 2001 | grams are [written in C] language. | |
| 11751232 | perl | MELTING, computing the melting temperature of nucleic acid duplex. | 2001 | n-source. [perl] scripts a | |
| 11751230 | c | A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. | 2001 | functions [written in C]. the scri | |
| 11751230 | mathlab | A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. | 2001 | products [matlab], s-plus, | |
| 11751227 | perl | How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. | 2001 | a [perl] implement | |
| 11724739 | perl | Database-driven multi locus sequence typing (MLST) of bacterial pathogens. | 2001 | a set of [perl] scripts f | |
| 11707150 | java | FastGroup: a program to dereplicate libraries of 16S rDNA sequences. | 2001 | tgroup, a [java] program d | |
| 11673244 | mathlab | Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. | 2001 | [matlab] (mathwork | |
| 11591214 | java | FOUNTAIN: a JAVA open-source package to assist large sequencing projects. | 2001 | untain: a [java] open-sour | |
| 11590102 | perl | GeneMachine: gene prediction and sequence annotation. | 2001 | suite of [perl] programs | |
| 11524384 | python | SIR: a simple indexing and retrieval system for biological flat file databases. | 2001 | ritten in [python]. since th | |
| 11524378 | c++ | Multi-query sequence BLAST output examination with MuSeqBox. | 2001 | standard [C++] and is fr | |
| 11524374 | c++ | The Bioinformatics Template Library--generic components for biocomputing. | 2001 | ndard for [C++] includes | |
| 11448890 | java | A Java applet for visualizing protein-protein interaction. | 2001 | a [java] applet fo | |
| 11448888 | java | PAL: an object-oriented programming library for molecular evolution and phylogenetics. | 2001 | ection of [java] classes f | |
| 11448887 | c | ADAPTSITE: detecting natural selection at single amino acid sites. | 2001 | urce code [written in C], binary f | |
| 11331235 | perl | Retrieval and on-the-fly alignment of sequence fragments from the HIV database. | 2001 | ection of [perl] scripts t | |
| 11301314 | java | ATV: display and manipulation of annotated phylogenetic trees. | 2001 | atv) is a [java] tool for | |
| 11301307 | java | J-Express: exploring gene expression data using Java. | 2001 | ata using [java]. | |
| 11301303 | java | NIFAS: visual analysis of domain evolution in proteins. | 2001 | a [java] applet, n | |
| 11238077 | perl | Virtual PCR. | 2001 | [perl] code and | |
| 11159329 | perl | Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. | 2000 | ped using [perl] and perl/ | |
| 11159311 | perl | Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions. | 2000 | irix 6.4, [perl] parsers, | |
| 11120685 | java | Artemis: sequence visualization and annotation. | 2000 | mented in [java], and can | |
| 11108704 | c++ | BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library. | 2000 | mework in [C++] that has | |
| 11038333 | python | Object-oriented parsing of biological databases with Python. | 2000 | ases with [python]. | |
| 10871272 | java | Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes. | 2000 | -friendly [java] gui. resu | |
| 10869040 | java | A browser for expression data. | 2000 | xtensible [java] applicati | |
| 10869029 | java | JESAM: CORBA software components to create and publish EST alignments and clusters. | 2000 | y example [java] applet br | |
| 10869029 | c++ | JESAM: CORBA software components to create and publish EST alignments and clusters. | 2000 | ll the c, [C++] and idl c | |
| 10869028 | perl | GABAagent: a system for integrating data on GABA receptors. | 2000 | ritten in [perl] script, a | |
| 10869022 | java | Storing biological sequence databases in relational form. | 2000 | perl and [java] in combin | |
| 10869022 | perl | Storing biological sequence databases in relational form. | 2000 | ons using [perl] and java | |
| 10869012 | c | Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. | 2000 | ritten in [ansi-C] and the t | |
| 10745985 | java | IMAGEne I: clustering and ranking of I.M.A.G.E. cDNA clones corresponding to known genes. | 1999 | intuitive [java] interface | |
| 10743559 | fortran | A simple algorithm for detecting circular permutations in proteins. | 1999 | a [fortran] program t | |
| 10743555 | perl | Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. | 1999 | set, the [perl] programs | |
| 10705440 | perl | MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters. | 1999 | stal is a [perl] script de | |
| 10705437 | java | ORBIT: an integrated environment for user-customized bioinformatics tools. | 1999 | upporting [java]. the syst | |
| 10705434 | r | An analysis of the Protein Data Bank in search of temporal and global trends. | 1999 | esolution [and R] value sho | |
| 10498781 | perl | Swissknife - 'lazy parsing' of SWISS-PROT entries. | 1999 | a set of [perl] modules w | |
| 10487877 | java | Interactive data input into the GeneNet database. | null | base, the [java] graphical | |
| 10366663 | java | JaDis: computing distances between nucleic acid sequences. | 1999 | adis is a [java] applicati | |
| 10366658 | java | CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences. | 1999 | awview, a [java] based vis | |
| 10320405 | java | CoPE: a collaborative pedigree drawing environment. | 1999 | ncludes a [java] program f | |
| 10320399 | java | DINAMO: interactive protein alignment and model building. | 1999 | web-based [java] applet at | |
| 10068695 | c++ | Genetic Simulation Library. | 1999 | a set of [C++] programs | |
| 9918957 | java | WEBMAP: radiation hybrid mapping on the WWW. | 1998 | a [java] interface | |
| 9918956 | perl | SPEM: a parser for EMBL style flat file database entries. | 1998 | a set of [perl] modules f | |
| 9918950 | java | Representing metabolic pathway information: an object-oriented approach. | 1998 | ped using [java], an objec | |
| 9789101 | java | A web server to locate periodicities in a sequence | 1998 | er with a [java] interface | |
| 9789101 | c++ | A web server to locate periodicities in a sequence | 1998 | ritten in [C++], which im | |
| 9789100 | java | A visual environment for the manipulation and integration of JAVA beans. | 1998 | ration of [java] beans. | |
| 9789091 | perl | GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. | 1998 | mpiled by [perl] scripts t | |
| 9730921 | perl | The LabBase system for data management in large scale biology research laboratories. | 1998 | ritten in [perl]. | |
| 9694997 | java | Graphical interface to the genetic network database GeNet. | 1998 | esigned a [java] applet wh | |
| 9694992 | java | GeneNet: a gene network database and its automated visualization. | 1998 | ritten in [java] provides | |
| 9694986 | java | The bio-objects project. Part I: the object data model core elements. | 1998 | aries and [java] binary fi | |
| 9694986 | c++ | The bio-objects project. Part I: the object data model core elements. | 1998 | assemble [C++] libraries | |
| 9694985 | c++ | Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library. | 1998 | nted as a [C++] object-or | |
| 9682060 | c | CloneIt: finding cloning strategies, in-frame deletions and frameshifts. | 1998 | ritten in [ansi-C] language, | |
| 9682055 | perl | Removing near-neighbour redundancy from large protein sequence collections. | 1998 | 90, and a [perl] script (n | |
| 9520496 | perl | The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining. | 1998 | suite of [perl] routines. | |
| 9183530 | c++ | Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis. | 1997 | lities of [C++] programmi | |
| 9146965 | perl | Hopper: software for automating data tracking and flow in DNA sequencing. | 1997 | a central [perl] program, | |
| 8872394 | fortran | IBIS version 3: an OSF/Motif-based interface for IBIS--integrated biological imaging system. | 1996 | ritten in [fortran] 77 for co | |
| 8744774 | c++ | Object-oriented sequence analysis: SCL--a C++ class library. | 1996 | s: scl--a [C++] class lib | |
| 8590181 | c | MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. | 1995 | is in the ['C'] language, | |
| 8590180 | c | Compression of protein sequence databases. | 1995 | interface [written in C] which all | |
| 8590169 | fortran | A FORTRAN program to simulate the evolution of genetic variability in a small population. | 1995 | a [fortran] program t | |
| 8521055 | c | DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences. | 1995 | ritten in [ansi-C] for pcs a | |
| 7796269 | fortran | Simulating efficiently the evolution of DNA sequences. | 1995 | nu-driven [fortran] programs | |
| 7704656 | c++ | Design and application of PDBlib, a C++ macromolecular class library. | 1994 | pdblib, a [C++] macromole | |
| 7828069 | fortran | A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins. | 1994 | ethods. a [fortran] program h | |
| 7528631 | c | Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. | 1994 | rogram is [written in C] using xvi | |
| 8019868 | c++ | MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. | 1994 | ritten in [C++] and is in | |
| 8143154 | c | FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies. | 1993 | en in the [C language] for unix | |
| 8293331 | c | A general UNIX interface for biocomputing and network information retrieval software. | 1993 | ogram was [written in C] language | |
| 7507400 | c | Automatic display of RNA secondary structures. | 1993 | programs [written in C] language | |
| 8402211 | c | SCAMP: a general-purpose simulator and metabolic control analysis program. | 1993 | rogram is [written in C] and is po | |
| 8481826 | c | A hypertext-like approach to navigating through the GCG sequence analysis package. | 1993 | en in the [C language] and using | |
| 1468016 | fortran | IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations. | 1992 | ritten in [fortran] 77 and ru | |
| 1422877 | c++ | METASIM: object-oriented modelling of cell regulation. | 1992 | itions in [C++] is presen | |
| 1633564 | c++ | Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system. | 1992 | rted into [C++], and then | |
| 1353007 | fortran | A microcomputer FORTRAN program for rapid determination of lethal concentrations of biocides in mosquito control. | 1992 | ocomputer [fortran] program f | |
| 1591615 | c | CLUSTAL V: improved software for multiple sequence alignment. | 1992 | which is [written in C] and can b | |
| 1568123 | fortran | MULTICOMP: a program package for multiple sequence comparison. | 1992 | mented in [fortran] 77 for va | |
| 2059852 | fortran | PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs. | 1991 | promot: a [fortran] program t | |
| 2059843 | fortran | Software for the development and evaluation of probabilistic identification matrices. | 1991 | ritten in [fortran] 77 and ca | |
| 2207751 | c | POLCA, a library running in a modern environment, implements a protocol for averaging randomly oriented images. | 1990 | polca is [written in C] and runs | |
| 2207747 | c | MUCIDS: an operative C environment for acquisition and processing of polarized-light scattered from biological specimens. | 1990 | tware was [written in C] lattice a | |
| 2207743 | c | A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity. | 1990 | re in the [language C]. new appl | |
| 2207743 | fortran | A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity. | 1990 | ritten in [fortran], is exten | |
| 2207741 | fortran | The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems. | 1990 | develop a [fortran] algorithm | |
| 2361183 | c | Olga--oligonucleotide primer design program for the Atari ST. | 1990 | standard ['C'] and makes | |
| 2310954 | fortran | Analysis of mixed lipid extracts using 1H NMR spectra. | 1990 | ts. a new [fortran] algorithm | |
| 2819513 | fortran | HYLAS: program for generating H curves (abstract three-dimensional representations of long DNA sequences). | 1989 | ritten in [fortran] with sepa | |
| 2766006 | fortran | A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations. | 1989 | a [fortran] subroutin | |
| 2924171 | fortran | SDSE: a software package to simulate the evolution of a pair of DNA sequences. | 1989 | eme. five [fortran] programs, | |
| 3208177 | fortran | A program for drawing evolutionary trees. | 1988 | ritten in [fortran] 66, which | |
| 3167604 | fortran | Computer program Jamsek combining statistical and stereochemical rules for the prediction of protein secondary structure. | 1988 | ritten in [fortran] for an ic | |
| 3167596 | fortran | A computer program to display codon changes caused by mutagenesis. | 1988 | a [fortran] program f | |
| 3453239 | fortran | A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes. | 1987 | ritten in [fortran] 77 to loc | |
| 3453234 | fortran | Interfacing similarity search software with the sequence retrieval system ACNUC. | 1987 | ritten in [fortran] 77 and is | |
| 3453230 | fortran | A modified Chou and Fasman protein structure algorithm. | 1987 | a [fortran] program p | |
| 3453213 | fortran | Programs for evaluating and characterising bacterial taxonomic data. | 1987 | ritten in [fortran] 77 and im | |
| 3453210 | c | Pattern matching of biological sequences with limited storage. | 1987 | mented in [C programming] language | |
| 3450370 | fortran | Visualization of the entire surface of a protein by cartographic projection. | 1986 | ritten in [fortran] iv (surfa | |
| 3450368 | fortran | An improved FORTRAN 77 recombinant DNA database management system with graphic extensions in GKS. | 1986 | improved [fortran] 77 recomb | |
| 3880341 | fortran | ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. | 1985 | ritten in [fortran] 77 which | |
| 3880336 | fortran | Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. | 1985 | describe [fortran] 77 softwa |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| .PHONY:all | |
| JVARKIT_HOME?=${HOME}/src/jvarkit-git/dist | |
| all: graph.png | |
| graph.png : biostar251002.tsv script.gnuplot | |
| grep -v YEAR $< | awk -F ' ' '{printf("%s\t%s\n",$$4,$$2);}'| tr " " "_" | grep -v null |\ | |
| sed 's/$$/ 1/'| ${HOME}/src/cmd-utils/src/yxv2table -a sum -n 0 | sed 's/^#/YEAR/' > graph.tsv && \ | |
| gnuplot script.gnuplot | |
| rm -f graph.tsv | |
| biostar251002.tsv : | |
| echo -e "PMID\tLANG\tTITLE\tYEAR\tCONTEXT" > $@ | |
| java -jar $(JVARKIT_HOME)/pubmeddump.jar 'Cabios[journal] OR Bioinformatics[journal]' |\ | |
| java -jar $(JVARKIT_HOME)/pubmedcodinglang.jar -c 2> /dev/null |tr '"' ' ' | tr '"' ' ' |\ | |
| tee /dev/tty >> $@ | |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| set terminal svg size 1000,800; | |
| set output "graph.svg" | |
| set title "Bioinformatics/language" | |
| set key invert reverse Left outside | |
| set key autotitle columnheader | |
| set yrange [0:] | |
| set auto x | |
| set datafile separator "\t" | |
| unset xtics | |
| set xlabel "Year" | |
| set ylabel "Count" | |
| set xtics nomirror rotate by -45 scale 0 | |
| set style data histogram | |
| set style histogram rowstacked | |
| set style fill solid border -1 | |
| set boxwidth 0.75 | |
| N=`awk 'NR==1 {print NF}' graph.tsv` | |
| plot 'graph.tsv' using 2:xtic(1), for [i=3:N] '' using i; | |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment