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Forum: Programming language use distribution from recent programs / articles https://www.biostars.org/p/251002/#251056 pubmed language code
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| -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 | |
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| 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 | |
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| 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 | |
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| 28166716 | python | PyHLA: tests for the association between HLA alleles and diseases. | 2017 | veloped a [python] package c | |
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| 28165109 | python | cyvcf2: fast, flexible variant analysis with Python. | 2017 | ysis with [python]. | |
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| 28158442 | python | Automated cell type discovery and classification through knowledge transfer. | 2017 | a [python] package ( | |
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| 28130227 | java | Unrealistic phylogenetic trees may improve phylogenetic footprinting. | 2017 | mented in [java] and can b | |
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| 28096085 | perl | Improved orthology inference with Hieranoid 2. | 2017 | [perl] code free | |
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| 28065901 | java | RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination. | 2017 | mented in [java], and is f | |
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| 28061750 | java | GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. | 2017 | tandalone [java] applicati | |
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| 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 | |
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| 28031184 | perl | SVScore: an impact prediction tool for structural variation. | 2017 | mented in [perl] and avail | |
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| 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 | |
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| 28003263 | r | bnstruct: an R package for Bayesian Network structure learning in the presence of missing data. | 2017 | truct: an [R package] for bayes | |
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| 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 | |
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| 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 | |
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| 27938331 | r | Robust multi-group gene set analysis with few replicates. | 2016 | nsive. an [R package] implement | |
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| 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 | |
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| 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 | |
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| 27797779 | java | JADOPPT: java based AutoDock preparing and processing tool. | 2017 | jadoppt: [java] based aut | |
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| 27797777 | python | INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. | 2017 | c ++ and [python]. full sou | |
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| 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 | |
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| 27794557 | python | FractBias: a graphical tool for assessing fractionation bias following polyploidy. | 2017 | able with [python] 2.7 or ip | |
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| 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 | |
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| 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 | |
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| 27766961 | python | VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. | 2016 | n c++ and [python], for read | |
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| 27766934 | r | CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints. | 2016 | the [R package] ccpromise | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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]. | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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]. | |
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| 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 | |
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| 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 | |
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| 26382193 | perl | ICT: isotope correction toolbox. | 2016 | language [perl] and, ther | |
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| 26085503 | python | libRoadRunner: a high performance SBML simulation and analysis library. | 2015 | rough its [python] interface | |
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| 26072509 | python | IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. | 2015 | a c++ and [python] program r | |
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| 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 | |
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| 26059717 | python | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. | 2015 | mented in [python] and datas | |
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| 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 | |
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| 26048599 | python | Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons. | 2015 | [python] code is a | |
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| 26026168 | r | lpNet: a linear programming approach to reconstruct signal transduction networks. | 2015 | ach as an [R package] available | |
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| 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 | |
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| 25987568 | python | TRAL: tandem repeat annotation library. | 2015 | en-source [python] 3 library | |
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| 25980407 | python | NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. | 2015 | en-source [python] module; b | |
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| 25940562 | java | HTT-DB: horizontally transferred transposable elements database. | 2015 | based on [java] and mysql | |
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| 25847006 | r | Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data. | 2015 | an [R package] to run a | |
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| 25644268 | r | CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data. | 2015 | from the [CRAN] repositor | |
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| 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 | |
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| 25380958 | r | Development of a robust classifier for quality control of reverse-phase protein arrays. | 2015 | percurve [R package], can be f | |
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| 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]. | |
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| 25371041 | r | Missing value imputation in high-dimensional phenomic data: imputable or not, and how? | 2014 | thods. an [R package] phenomei | |
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| 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 | |
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| 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 | |
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| 24669753 | c++ | FreeContact: fast and free software for protein contact prediction from residue co-evolution. | 2014 | the free [C++] library | |
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| 24659106 | c++ | Improved transcript isoform discovery using ORF graphs. | 2014 | ilable as [C++] source co | |
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| 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 | |
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| 24642064 | perl | KAnalyze: a fast versatile pipelined k-mer toolkit. | 2014 | built on [perl] and linux | |
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| 24642061 | r | An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). | 2014 | an [R package] to analys | |
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| 24618465 | java | A personalized committee classification approach to improving prediction of breast cancer metastasis. | 2014 | atlab and [java] available | |
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| 24603985 | python | PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. | 2014 | ritten in [python] and freel | |
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| 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 | |
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| 24567544 | javascript | jHeatmap: an interactive heatmap viewer for the web. | 2014 | adaptable [javascript] library d | |
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| 24470574 | c++ | PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. | 2014 | ython and [C++]. it bundl | |
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| 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 | |
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| 24177720 | mathlab | MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. | 2014 | tworks in [matlab] using mai | |
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| 24167158 | r | Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. | 2014 | the [R package] 'directpa | |
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| 23962281 | python | Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters. | 2013 | mented in [python], and are | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 25969751 | perl | Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification. | 2012 | elamp, a [perl] script, w | |
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| 22135419 | java | DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments. | 2012 | dman: a [java] tool for | |
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| 22110245 | java | PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. | 2012 | spider, a [java] program t | |
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| 22072386 | java | Wavelet-based image fusion in multi-view three-dimensional microscopy. | 2012 | eloped in [java]. the soft | |
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| 22072385 | python | MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. | 2012 | ble and a [python] script th | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 19289444 | python | GS2: an efficiently computable measure of GO-based similarity of gene sets. | 2009 | en-source [python] library. | |
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| 19040729 | r | Highly sensitive feature detection for high resolution LC/MS. | 2008 | into the [Bioconductor] r-package | |
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| 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 | |
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| 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 | |
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| 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 | |
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| 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 |
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| .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 >> $@ | |
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| 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; | |
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