R-bundle-Bioconductor¶
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
https://bioconductor.org
Available modules¶
The overview below shows which R-bundle-Bioconductor installations are available per target architecture in EESSI, ordered based on software version (new to old).
To start using R-bundle-Bioconductor, load one of these modules using a module load command like:
(This data was automatically generated on Thu, 12 Sep 2024 at 12:39:49 UTC)
| aarch64/generic | aarch64/neoverse_n1 | aarch64/neoverse_v1 | x86_64/generic | x86_64/amd/zen2 | x86_64/amd/zen3 | x86_64/amd/zen4 | x86_64/intel/haswell | x86_64/intel/skylake_avx512 | |
|---|---|---|---|---|---|---|---|---|---|
| R-bundle-Bioconductor/3.18-foss-2023a-R-4.3.2 | x | x | x | x | x | x | x | x | x |
| R-bundle-Bioconductor/3.16-foss-2022b-R-4.2.2 | x | x | x | x | x | x | - | x | x |
R-bundle-Bioconductor/3.18-foss-2023a-R-4.3.2¶
This is a list of extensions included in the module:
affxparser-1.74.0, affy-1.80.0, affycoretools-1.74.0, affyio-1.72.0, AgiMicroRna-2.52.0, agricolae-1.3-7, ALDEx2-1.34.0, ALL-1.44.0, ANCOMBC-2.4.0, annaffy-1.74.0, annotate-1.80.0, AnnotationDbi-1.64.1, AnnotationFilter-1.26.0, AnnotationForge-1.44.0, AnnotationHub-3.10.0, anytime-0.3.9, aroma.affymetrix-3.2.1, aroma.apd-0.7.0, aroma.core-3.3.0, aroma.light-3.32.0, ash-1.0-15, ATACseqQC-1.26.0, AUCell-1.24.0, aws.s3-0.3.21, aws.signature-0.6.0, babelgene-22.9, ballgown-2.34.0, basilisk-1.14.2, basilisk.utils-1.14.1, batchelor-1.18.1, baySeq-2.36.0, beachmat-2.18.0, BH-1.84.0-0, Biobase-2.62.0, BiocBaseUtils-1.4.0, BiocFileCache-2.10.1, BiocGenerics-0.48.0, BiocIO-1.12.0, BiocManager-1.30.22, BiocNeighbors-1.20.2, BiocParallel-1.36.0, BiocSingular-1.18.0, BiocStyle-2.30.0, BiocVersion-3.18.1, biomaRt-2.58.0, biomformat-1.30.0, Biostrings-2.70.0, biovizBase-1.50.0, blme-1.0-5, bluster-1.12.0, bookdown-0.37, BSgenome-1.70.1, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bsseq-1.38.0, bumphunter-1.44.0, ca-0.71.1, CAGEfightR-1.22.0, CAGEr-2.8.0, CAMERA-1.58.0, Category-2.68.0, ccdata-1.28.0, ccmap-1.28.0, CGHbase-1.62.0, CGHcall-2.64.0, ChIPpeakAnno-3.36.0, chromVAR-1.24.0, clusterProfiler-4.10.0, CNEr-1.38.0, coloc-5.2.3, colorRamps-2.3.1, ComplexHeatmap-2.18.0, ConsensusClusterPlus-1.66.0, conumee-1.36.0, crossmeta-1.28.0, cummeRbund-2.44.0, cytolib-2.14.1, CytoML-2.14.0, dada2-1.30.0, ddPCRclust-1.22.0, DECIPHER-2.30.0, DeconRNASeq-1.44.0, decontam-1.22.0, decoupleR-2.8.0, DEGseq-1.56.1, DelayedArray-0.28.0, DelayedMatrixStats-1.24.0, densEstBayes-1.0-2.2, derfinder-1.36.0, derfinderHelper-1.36.0, DESeq2-1.42.0, diffcyt-1.22.0, dir.expiry-1.10.0, directlabels-2024.1.21, DirichletMultinomial-1.44.0, DNABarcodes-1.32.0, DNAcopy-1.76.0, DO.db-2.9, docopt-0.7.1, DOSE-3.28.2, dqrng-0.3.2, DRIMSeq-1.30.0, DropletUtils-1.22.0, DSS-2.50.1, dupRadar-1.32.0, DynDoc-1.80.0, EBImage-4.44.0, edgeR-4.0.12, egg-0.4.5, emmeans-1.10.0, enrichplot-1.22.0, EnsDb.Hsapiens.v75-2.99.0, EnsDb.Hsapiens.v79-2.99.0, EnsDb.Hsapiens.v86-2.99.0, ensembldb-2.26.0, escape-1.12.0, estimability-1.4.1, ExperimentHub-2.10.0, extraDistr-1.10.0, factoextra-1.0.7, fANCOVA-0.6-1, fda-6.1.4, FDb.InfiniumMethylation.hg19-2.2.0, fds-1.8, feature-1.2.15, fgsea-1.28.0, filelock-1.0.3, flowAI-1.32.0, flowClean-1.40.0, flowClust-3.40.0, flowCore-2.14.0, flowDensity-1.36.1, flowFP-1.60.0, flowMerge-2.50.0, flowPeaks-1.48.0, FlowSOM-2.10.0, FlowSorted.Blood.EPIC-2.6.0, FlowSorted.CordBloodCombined.450k-1.18.0, flowStats-4.14.1, flowViz-1.66.0, flowWorkspace-4.14.2, FRASER-1.14.0, fresh-0.2.0, gcrma-2.74.0, gdsfmt-1.38.0, genefilter-1.84.0, geneLenDataBase-1.38.0, geneplotter-1.80.0, GENESIS-2.32.0, GENIE3-1.24.0, GenomeInfoDb-1.38.5, GenomeInfoDbData-1.2.11, GenomicAlignments-1.38.2, GenomicFeatures-1.54.1, GenomicFiles-1.38.0, GenomicInteractions-1.36.0, GenomicRanges-1.54.1, GenomicScores-2.14.3, GEOmap-2.5-5, GEOquery-2.70.0, ggbio-1.50.0, ggcyto-1.30.0, ggdendro-0.1.23, ggnewscale-0.4.9, ggpointdensity-0.1.0, ggrastr-1.0.2, ggseqlogo-0.1, ggthemes-5.0.0, ggtree-3.10.0, GLAD-2.66.0, Glimma-2.12.0, GlobalAncova-4.20.0, globaltest-5.56.0, GO.db-3.18.0, GOSemSim-2.28.1, goseq-1.54.0, GOstats-2.68.0, graph-1.80.0, graphite-1.48.0, GSEABase-1.64.0, gsmoothr-0.1.7, gson-0.1.0, GSVA-1.50.0, Gviz-1.46.1, GWASExactHW-1.01, GWASTools-1.48.0, HDF5Array-1.30.0, HDO.db-0.99.1, hdrcde-3.4, heatmaply-1.5.0, hgu133plus2.db-3.13.0, HiCBricks-1.20.0, HiCcompare-1.24.0, HMMcopy-1.44.0, Homo.sapiens-1.3.1, IHW-1.30.0, IlluminaHumanMethylation450kanno.ilmn12.hg19-0.6.1, IlluminaHumanMethylation450kmanifest-0.4.0, IlluminaHumanMethylationEPICanno.ilm10b2.hg19-0.6.0, IlluminaHumanMethylationEPICanno.ilm10b4.hg19-0.6.0, IlluminaHumanMethylationEPICmanifest-0.3.0, illuminaio-0.44.0, impute-1.76.0, InteractionSet-1.30.0, interactiveDisplayBase-1.40.0, intervals-0.15.4, IRanges-2.36.0, isva-1.9, JASPAR2020-0.99.10, KEGGgraph-1.62.0, KEGGREST-1.42.0, LEA-3.14.0, limma-3.58.1, log4r-0.4.3, lpsymphony-1.30.0, lsa-0.73.3, lumi-2.54.0, M3Drop-1.28.0, marray-1.80.0, maSigPro-1.74.0, MassSpecWavelet-1.68.0, MatrixGenerics-1.14.0, MBA-0.1-0, MEDIPS-1.54.0, MetaboCoreUtils-1.10.0, metagenomeSeq-1.43.0, metaMA-3.1.3, metap-1.9, metapod-1.10.1, MethylSeekR-1.42.0, methylumi-2.48.0, Mfuzz-2.62.0, mia-1.10.0, minfi-1.48.0, missMethyl-1.36.0, mixOmics-6.26.0, mixsqp-0.3-54, MLInterfaces-1.82.0, MotifDb-1.44.0, motifmatchr-1.24.0, motifStack-1.46.0, MsCoreUtils-1.14.1, MsExperiment-1.4.0, MsFeatures-1.10.0, msigdbr-7.5.1, MSnbase-2.28.1, MSstats-4.10.0, MSstatsConvert-1.12.0, MSstatsLiP-1.8.1, MSstatsPTM-2.4.2, MSstatsTMT-2.10.0, MultiAssayExperiment-1.28.0, MultiDataSet-1.30.0, multtest-2.58.0, muscat-1.16.0, mutoss-0.1-13, mzID-1.40.0, mzR-2.36.0, NADA-1.6-1.1, ncdfFlow-2.48.0, NMF-0.26, NOISeq-2.46.0, numbat-1.3.2-1, oligo-1.66.0, oligoClasses-1.64.0, ontologyIndex-2.11, oompaBase-3.2.9, oompaData-3.1.3, openCyto-2.14.0, org.Hs.eg.db-3.18.0, org.Mm.eg.db-3.18.0, org.Rn.eg.db-3.18.0, OrganismDbi-1.44.0, OUTRIDER-1.20.0, pathview-1.42.0, pcaMethods-1.94.0, perm-1.0-0.4, PFAM.db-3.18.0, phyloseq-1.46.0, plyranges-1.22.0, pmp-1.14.0, polyester-1.38.0, poweRlaw-0.70.6, preprocessCore-1.64.0, pRoloc-1.42.0, pRolocdata-1.40.0, pRolocGUI-2.12.0, ProtGenerics-1.34.0, PRROC-1.3.1, PSCBS-0.66.0, PureCN-2.8.1, qap-0.1-2, QDNAseq-1.38.0, QFeatures-1.12.0, qlcMatrix-0.9.7, qqconf-1.3.2, quantsmooth-1.68.0, qvalue-2.34.0, R.devices-2.17.1, R.filesets-2.15.0, R.huge-0.10.1, rainbow-3.8, randomcoloR-1.1.0.1, rARPACK-0.11-0, RBGL-1.78.0, RcisTarget-1.22.0, RcppAnnoy-0.0.22, RcppHNSW-0.5.0, RcppML-0.3.7, RcppZiggurat-0.1.6, reactome.db-1.86.2, ReactomePA-1.46.0, regioneR-1.34.0, reldist-1.7-2, remaCor-0.0.16, Repitools-1.48.0, ReportingTools-2.42.3, ResidualMatrix-1.12.0, restfulr-0.0.15, Rfast-2.1.0, RFOC-3.4-10, rGADEM-2.50.0, Rgraphviz-2.46.0, rhdf5-2.46.1, rhdf5filters-1.14.1, Rhdf5lib-1.24.1, Rhtslib-2.4.1, Ringo-1.66.0, RNASeqPower-1.42.0, RnBeads-2.20.0, RnBeads.hg19-1.34.0, RnBeads.hg38-1.34.0, RnBeads.mm10-2.10.0, RnBeads.mm9-1.34.0, RnBeads.rn5-1.34.0, ROC-1.78.0, rols-2.30.0, ROntoTools-2.30.0, ropls-1.34.0, RPMG-2.2-7, RProtoBufLib-2.14.0, Rsamtools-2.18.0, RSEIS-4.1-6, Rsubread-2.16.1, rsvd-1.0.5, rtracklayer-1.62.0, Rwave-2.6-5, S4Arrays-1.2.0, S4Vectors-0.40.2, samr-3.0, SamSPECTRAL-1.56.0, SC3-1.30.0, ScaledMatrix-1.10.0, SCANVIS-1.16.0, scater-1.30.1, scattermore-1.2, scDblFinder-1.16.0, scistreer-1.2.0, scran-1.30.2, scrime-1.3.5, scuttle-1.12.0, SeqArray-1.42.0, seqLogo-1.68.0, SeqVarTools-1.40.0, seriation-1.5.4, Seurat-5.0.1, SeuratObject-5.0.1, shinyBS-0.61.1, shinydashboardPlus-2.0.3, shinyFiles-0.9.3, shinyhelper-0.3.2, shinypanel-0.1.5, shinyWidgets-0.8.1, ShortRead-1.60.0, siggenes-1.76.0, Signac-1.12.0, simplifyEnrichment-1.12.0, SingleCellExperiment-1.24.0, SingleR-2.4.1, sitmo-2.0.2, slingshot-2.10.0, SMVar-1.3.4, SNPRelate-1.36.0, snpStats-1.52.0, SparseArray-1.2.3, sparseMatrixStats-1.14.0, sparsesvd-0.2-2, SpatialExperiment-1.12.0, Spectra-1.12.0, SPIA-2.54.0, splancs-2.01-44, SPOTlight-1.6.7, stageR-1.24.0, struct-1.14.0, structToolbox-1.14.0, SummarizedExperiment-1.32.0, susieR-0.12.35, sva-3.50.0, TailRank-3.2.2, TFBSTools-1.40.0, TFMPvalue-0.0.9, tkWidgets-1.80.0, TrajectoryUtils-1.10.0, treeio-1.26.0, TreeSummarizedExperiment-2.10.0, TSP-1.2-4, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0, tximport-1.30.0, UCell-2.6.2, uwot-0.1.16, variancePartition-1.32.2, VariantAnnotation-1.48.1, venn-1.12, vsn-3.70.0, waiter-0.2.5, wateRmelon-2.8.0, WGCNA-1.72-5, widgetTools-1.80.0, Wrench-1.20.0, xcms-4.0.2, XVector-0.42.0, zCompositions-1.5.0-1, zellkonverter-1.12.1, zlibbioc-1.48.0
R-bundle-Bioconductor/3.16-foss-2022b-R-4.2.2¶
This is a list of extensions included in the module:
affxparser-1.70.0, affy-1.76.0, affycoretools-1.70.0, affyio-1.68.0, AgiMicroRna-2.48.0, agricolae-1.3-5, ALDEx2-1.30.0, ALL-1.40.0, ANCOMBC-2.0.2, annaffy-1.70.0, annotate-1.76.0, AnnotationDbi-1.60.2, AnnotationFilter-1.22.0, AnnotationForge-1.40.1, AnnotationHub-3.6.0, anytime-0.3.9, aroma.affymetrix-3.2.1, aroma.apd-0.6.1, aroma.core-3.3.0, aroma.light-3.28.0, ash-1.0-15, ATACseqQC-1.22.0, AUCell-1.20.2, aws.s3-0.3.21, aws.signature-0.6.0, babelgene-22.9, ballgown-2.30.0, basilisk-1.10.2, basilisk.utils-1.10.0, batchelor-1.14.1, baySeq-2.31.0, beachmat-2.14.0, Biobase-2.58.0, BiocBaseUtils-1.0.0, BiocFileCache-2.6.1, BiocGenerics-0.44.0, BiocIO-1.8.0, BiocManager-1.30.20, BiocNeighbors-1.16.0, BiocParallel-1.32.5, BiocSingular-1.14.0, BiocStyle-2.26.0, BiocVersion-3.16.0, biomaRt-2.54.0, biomformat-1.26.0, Biostrings-2.66.0, biovizBase-1.46.0, blme-1.0-5, bluster-1.8.0, bookdown-0.33, BSgenome-1.66.3, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bsseq-1.34.0, bumphunter-1.40.0, ca-0.71.1, CAGEr-2.4.0, CAMERA-1.54.0, Category-2.64.0, ccdata-1.24.0, ccmap-1.24.0, CGHbase-1.58.0, CGHcall-2.60.0, ChIPpeakAnno-3.32.0, chromVAR-1.20.2, clusterProfiler-4.6.2, CNEr-1.34.0, coloc-5.1.0.1, colorRamps-2.3.1, ComplexHeatmap-2.14.0, ConsensusClusterPlus-1.62.0, conumee-1.32.0, crossmeta-1.24.0, cummeRbund-2.40.0, cytolib-2.10.1, CytoML-2.10.0, dada2-1.26.0, ddPCRclust-1.18.0, DECIPHER-2.26.0, DeconRNASeq-1.40.0, decontam-1.18.0, decoupleR-2.4.0, DEGseq-1.52.0, DelayedArray-0.24.0, DelayedMatrixStats-1.20.0, densEstBayes-1.0-2.1, derfinder-1.32.0, derfinderHelper-1.32.0, DESeq2-1.38.3, diffcyt-1.18.0, dir.expiry-1.6.0, DirichletMultinomial-1.40.0, DNABarcodes-1.28.0, DNAcopy-1.72.3, DO.db-2.9, docopt-0.7.1, DOSE-3.24.2, dqrng-0.3.0, DRIMSeq-1.26.0, DropletUtils-1.18.1, DSS-2.46.0, dupRadar-1.28.0, DynDoc-1.76.0, EBImage-4.40.0, edgeR-3.40.2, egg-0.4.5, emmeans-1.8.5, enrichplot-1.18.3, EnsDb.Hsapiens.v75-2.99.0, EnsDb.Hsapiens.v79-2.99.0, EnsDb.Hsapiens.v86-2.99.0, ensembldb-2.22.0, escape-1.8.0, estimability-1.4.1, ExperimentHub-2.6.0, extraDistr-1.9.1, factoextra-1.0.7, fda-6.0.5, FDb.InfiniumMethylation.hg19-2.2.0, fds-1.8, feature-1.2.15, fgsea-1.24.0, filelock-1.0.2, flowAI-1.28.0, flowClean-1.36.0, flowClust-3.36.0, flowCore-2.10.0, flowDensity-1.32.0, flowFP-1.56.3, flowMerge-2.46.0, flowPeaks-1.44.0, FlowSOM-2.6.0, FlowSorted.Blood.EPIC-2.2.0, FlowSorted.CordBloodCombined.450k-1.14.0, flowStats-4.10.0, flowViz-1.62.0, flowWorkspace-4.10.1, FRASER-1.10.2, fresh-0.2.0, gcrma-2.70.0, gdsfmt-1.34.0, genefilter-1.80.3, geneLenDataBase-1.34.0, geneplotter-1.76.0, GENESIS-2.28.0, GENIE3-1.20.0, GenomeInfoDb-1.34.9, GenomeInfoDbData-1.2.9, GenomicAlignments-1.34.1, GenomicFeatures-1.50.4, GenomicFiles-1.34.0, GenomicRanges-1.50.2, GenomicScores-2.10.0, GEOmap-2.5-0, GEOquery-2.66.0, ggbio-1.46.0, ggcyto-1.26.4, ggdendro-0.1.23, ggnewscale-0.4.8, ggpointdensity-0.1.0, ggrastr-1.0.1, ggseqlogo-0.1, ggthemes-4.2.4, ggtree-3.6.2, GLAD-2.62.0, Glimma-2.8.0, GlobalAncova-4.16.0, globaltest-5.52.0, GO.db-3.16.0, GOSemSim-2.24.0, goseq-1.50.0, GOstats-2.64.0, graph-1.76.0, graphite-1.44.0, GSEABase-1.60.0, gsmoothr-0.1.7, gson-0.1.0, GSVA-1.46.0, Gviz-1.42.1, GWASExactHW-1.01, GWASTools-1.44.0, HDF5Array-1.26.0, HDO.db-0.99.1, hdrcde-3.4, heatmaply-1.4.2, hgu133plus2.db-3.13.0, HiCBricks-1.16.0, HiCcompare-1.20.0, HMMcopy-1.40.0, Homo.sapiens-1.3.1, IHW-1.26.0, IlluminaHumanMethylation450kanno.ilmn12.hg19-0.6.1, IlluminaHumanMethylation450kmanifest-0.4.0, IlluminaHumanMethylationEPICanno.ilm10b2.hg19-0.6.0, IlluminaHumanMethylationEPICanno.ilm10b4.hg19-0.6.0, IlluminaHumanMethylationEPICmanifest-0.3.0, illuminaio-0.40.0, impute-1.72.3, InteractionSet-1.26.1, interactiveDisplayBase-1.36.0, intervals-0.15.4, IRanges-2.32.0, isva-1.9, JASPAR2020-0.99.10, KEGGgraph-1.58.3, KEGGREST-1.38.0, LEA-3.10.2, limma-3.54.2, log4r-0.4.3, lpsymphony-1.26.3, lsa-0.73.3, lumi-2.50.0, M3Drop-1.24.0, marray-1.76.0, maSigPro-1.70.0, MassSpecWavelet-1.64.1, MatrixGenerics-1.10.0, MBA-0.1-0, MEDIPS-1.50.0, metagenomeSeq-1.40.0, metaMA-3.1.3, metap-1.8, metapod-1.6.0, MethylSeekR-1.38.0, methylumi-2.44.0, Mfuzz-2.58.0, mia-1.6.0, minfi-1.44.0, missMethyl-1.32.0, mixOmics-6.22.0, mixsqp-0.3-48, MLInterfaces-1.78.0, MotifDb-1.40.0, motifmatchr-1.20.0, motifStack-1.42.0, MsCoreUtils-1.10.0, MsFeatures-1.6.0, msigdbr-7.5.1, MSnbase-2.24.2, MSstats-4.6.5, MSstatsConvert-1.8.3, MSstatsLiP-1.4.1, MSstatsPTM-2.0.3, MSstatsTMT-2.6.1, MultiAssayExperiment-1.24.0, MultiDataSet-1.26.0, multtest-2.54.0, muscat-1.12.1, mutoss-0.1-13, mzID-1.36.0, mzR-2.32.0, NADA-1.6-1.1, ncdfFlow-2.44.0, NMF-0.25, NOISeq-2.42.0, numbat-1.2.2, oligo-1.62.2, oligoClasses-1.60.0, ontologyIndex-2.10, oompaBase-3.2.9, oompaData-3.1.3, openCyto-2.10.1, org.Hs.eg.db-3.16.0, org.Mm.eg.db-3.16.0, org.Rn.eg.db-3.16.0, OrganismDbi-1.40.0, OUTRIDER-1.16.3, 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