Last active
May 10, 2019 23:01
-
-
Save glin/cff301d2fac11e69a85135b802ed785d to your computer and use it in GitHub Desktop.
Get CRAN packages with Bioconductor dependencies
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Get a list of all CRAN packages with Bioc dependencies | |
| cran_bioc_pkgs <- function(bioc_repo = "https://bioconductor.org/packages/3.8/bioc", recursive = TRUE) { | |
| bioc_pkgs <- rownames(available.packages(repos = bioc_repo, filters = list())) | |
| unique(unlist(tools::package_dependencies(bioc_pkgs, reverse = TRUE, recursive = recursive))) | |
| } | |
| # Set a CRAN repo if necessary | |
| options(repos = "https://cloud.r-project.org") | |
| pkgs <- sort(cran_bioc_pkgs()) | |
| writeLines(pkgs) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ACNE | |
| AbsFilterGSEA | |
| ActiveDriverWGS | |
| ArrayBin | |
| AssayCorrector | |
| BACA | |
| BALCONY | |
| BASiNET | |
| BPM | |
| BayesNetBP | |
| BcDiag | |
| BiDAG | |
| BiSEp | |
| BinQuasi | |
| BioMedR | |
| BonEV | |
| Brundle | |
| CNVScope | |
| CONDOP | |
| CORM | |
| CSESA | |
| CSFA | |
| CSclone | |
| CVR | |
| Cascade | |
| CePa | |
| ClassComparison | |
| ClassDiscovery | |
| CleanBSequences | |
| CodeDepends | |
| CorrectOverloadedPeaks | |
| CrossValidate | |
| CrypticIBDcheck | |
| DAAGbio | |
| DCA | |
| DCD | |
| DCGL | |
| DCchoice | |
| DEVis | |
| DGCA | |
| DNLC | |
| DRomics | |
| DiffCorr | |
| DrInsight | |
| EMA | |
| EncDNA | |
| EstMix | |
| EthSEQ | |
| ExomeDepth | |
| FAMT | |
| FHtest | |
| FunctionalNetworks | |
| GExMap | |
| GLSE | |
| GMMAT | |
| GOGANPA | |
| GREP2 | |
| GSAgm | |
| GUIProfiler | |
| GenAlgo | |
| GenomicTools | |
| GenomicTools.fileHandler | |
| GiNA | |
| HDMT | |
| HEMDAG | |
| HTSCluster | |
| HTSSIP | |
| HeritSeq | |
| HiCblock | |
| HiCfeat | |
| HiCglmi | |
| HiResTEC | |
| ICDS | |
| IMaGES | |
| INCATome | |
| IntClust | |
| IntegratedJM | |
| InterpretMSSpectrum | |
| IsoGene | |
| KANT | |
| LANDD | |
| LDheatmap | |
| LOST | |
| LPGraph | |
| LipidMS | |
| MEET | |
| MM2S | |
| MM2Sdata | |
| MMDvariance | |
| MRPC | |
| MSIseq | |
| MSeasy | |
| MSeasyTkGUI | |
| MetaIntegrator | |
| MetaLonDA | |
| MetaPath | |
| MetabolomicsBasics | |
| MetamapsDB | |
| Miso | |
| Modeler | |
| MoonFinder | |
| NAPPA | |
| NBLDA | |
| NBPSeq | |
| NFP | |
| NIPTeR | |
| NPMOD | |
| NanoStringNorm | |
| NetPreProc | |
| NormalizeMets | |
| PCA4you | |
| PCDimension | |
| PCGSE | |
| PCS | |
| PMA | |
| PSCBS | |
| PairViz | |
| ParDNAcopy | |
| PepPrep | |
| PerfMeas | |
| PerseusR | |
| PhViD | |
| PhenotypeSimulator | |
| PlasmaMutationDetector | |
| QuACN | |
| R.SamBada | |
| R2GUESS | |
| RAMClustR | |
| RANKS | |
| RAPIDR | |
| REIDS | |
| RPPanalyzer | |
| RSNPset | |
| RSeed | |
| RVAideMemoire | |
| RcmdrPlugin.BiclustGUI | |
| Rnmr1D | |
| RobLox | |
| RobLoxBioC | |
| RockFab | |
| SID | |
| SIGN | |
| SMITIDstruct | |
| SPreFuGED | |
| SQDA | |
| STRAH | |
| STRMPS | |
| STraTUS | |
| SafeQuant | |
| SegCorr | |
| SeqFeatR | |
| SeqGrapheR | |
| ShinyImage | |
| SigTree | |
| SimRAD | |
| SimReg | |
| Sky | |
| SmartSVA | |
| SourceSet | |
| StroupGLMM | |
| SubVis | |
| SubpathwayLNCE | |
| TCGA2STAT | |
| TGS | |
| TROM | |
| TailRank | |
| TcGSA | |
| Thresher | |
| Tnseq | |
| TriadSim | |
| VSE | |
| WGCNA | |
| XGR | |
| YuGene | |
| adaptiveGPCA | |
| apmsWAPP | |
| armada | |
| aroma.affymetrix | |
| aroma.cn | |
| aroma.core | |
| babel | |
| bapred | |
| beadarrayFilter | |
| beadarrayMSV | |
| beadplexr | |
| binneR | |
| bioOED | |
| bioRad | |
| biofiles | |
| bioimagetools | |
| biomartr | |
| biospear | |
| bnspatial | |
| bootsPLS | |
| caRpools | |
| calmate | |
| cancerGI | |
| cate | |
| ceg | |
| cghRA | |
| classGraph | |
| cliqueMS | |
| clustDRM | |
| cogmapr | |
| coloc | |
| compendiumdb | |
| countToFPKM | |
| countTransformers | |
| cp4p | |
| crmn | |
| dGAselID | |
| dSVA | |
| dartR | |
| dc3net | |
| dcGOR | |
| deconstructSigs | |
| demi | |
| diffMeanVar | |
| dlsem | |
| dnet | |
| ePCR | |
| eclust | |
| edgeRun | |
| empiricalFDR.DESeq2 | |
| enviGCMS | |
| eulerian | |
| exp2flux | |
| fdrDiscreteNull | |
| flowDiv | |
| funbarRF | |
| g2f | |
| gRain | |
| gRbase | |
| gRc | |
| gRim | |
| genBaRcode | |
| genBart | |
| geneNetBP | |
| geno2proteo | |
| gitter | |
| gkmSVM | |
| gridDebug | |
| gridGraphviz | |
| groupedSurv | |
| harrietr | |
| hasseDiagram | |
| hddplot | |
| histry | |
| hoardeR | |
| hpoPlot | |
| iC10 | |
| iRefR | |
| icensBKL | |
| iheatmapr | |
| imputeLCMD | |
| interval | |
| ionflows | |
| isva | |
| jaccard | |
| jackstraw | |
| jetset | |
| jointseg | |
| kangar00 | |
| kmeRs | |
| kpcalg | |
| ktspair | |
| leapp | |
| lmQCM | |
| mDAG | |
| mExplorer | |
| mGSZ | |
| maGUI | |
| makeParallel | |
| mcmcabn | |
| metaMA | |
| metaboGSE | |
| metacoder | |
| metagear | |
| mglR | |
| miRtest | |
| mixKernel | |
| modeest | |
| moduleColor | |
| mppR | |
| msSurv | |
| multiDimBio | |
| mutoss | |
| mutossGUI | |
| mvgraphnorm | |
| myTAI | |
| netgsa | |
| netgwas | |
| nlcv | |
| noise | |
| nucim | |
| omu | |
| ontologyPlot | |
| orQA | |
| pRF | |
| pathfindR | |
| pcalg | |
| pcgen | |
| peakPantheR | |
| permGPU | |
| petro.One | |
| phantom | |
| plfMA | |
| plsRcox | |
| polyPK | |
| polyRAD | |
| poolVIM | |
| propOverlap | |
| protiq | |
| ptmixed | |
| qtlnet | |
| rJPSGCS | |
| rags2ridges | |
| ragt2ridges | |
| restfulr | |
| robustSingleCell | |
| roprov | |
| rsolr | |
| saasCNV | |
| samr | |
| santaR | |
| scBio | |
| scRNAtools | |
| scmamp | |
| sequenza | |
| sgPLS | |
| sigQC | |
| simMP | |
| simPATHy | |
| smapr | |
| smartdata | |
| snpEnrichment | |
| snpReady | |
| snpStatsWriter | |
| snplist | |
| speaq | |
| specmine | |
| spectralAnalysis | |
| spp | |
| ssizeRNA | |
| stablespec | |
| structSSI | |
| strum | |
| superbiclust | |
| survJamda | |
| survivALL | |
| swamp | |
| synbreed | |
| theseus | |
| tidygenomics | |
| topologyGSA | |
| trackr | |
| treeDA | |
| ttScreening | |
| uCAREChemSuiteCLI | |
| unifDAG | |
| wilson | |
| xseq | |
| zenplots |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment