R-bundle-Bioconductor 3.17-foss-2022b-R-4.3.1

Unsupported: Use of this version of R-bundle-Bioconductor is not supported. More information on our Applications Support and Retention Policy.

R is a free software environment for statistical computing and graphics.

Accessing R-bundle-Bioconductor 3.17-foss-2022b-R-4.3.1

To load the module for R-bundle-Bioconductor 3.17-foss-2022b-R-4.3.1 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps-unsupported/handbuilt/2019
module load R-bundle-Bioconductor/3.17-foss-2022b-R-4.3.1

BEAR Apps Version

2019h

Extensions

  • affxparser 1.72.0
  • affy 1.78.0
  • affycoretools 1.72.0
  • affyio 1.70.0
  • AgiMicroRna 2.50.0
  • agricolae-1.3-6
  • ALDEx2 1.32.0
  • ALL 1.42.0
  • ANCOMBC 2.2.1
  • annaffy 1.72.0
  • annotate 1.78.0
  • AnnotationDbi 1.62.2
  • AnnotationFilter 1.24.0
  • AnnotationForge 1.42.2
  • AnnotationHub 3.8.0
  • anytime 0.3.9
  • aroma.affymetrix 3.2.1
  • aroma.apd 0.7.0
  • aroma.core 3.3.0
  • aroma.light 3.30.0
  • ash-1.0-15
  • ATACseqQC 1.24.0
  • AUCell 1.22.0
  • aws.s3 0.3.21
  • aws.signature 0.6.0
  • ballgown 2.32.0
  • basilisk 1.12.1
  • basilisk.utils 1.12.1
  • batchelor 1.16.0
  • beachmat 2.16.0
  • Biobase 2.60.0
  • BiocBaseUtils 1.2.0
  • BiocFileCache 2.8.0
  • BiocGenerics 0.46.0
  • BiocIO 1.10.0
  • BiocManager 1.30.21
  • BiocNeighbors 1.18.0
  • BiocParallel 1.34.2
  • BiocSingular 1.16.0
  • BiocStyle 2.28.0
  • BiocVersion 3.17.1
  • biomaRt 2.56.1
  • biomformat 1.28.0
  • Biostrings 2.68.1
  • biovizBase 1.48.0
  • blme-1.0-5
  • bluster 1.10.0
  • bookdown 0.34
  • BSgenome 1.68.0
  • 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 1.36.0
  • bumphunter 1.42.0
  • ca 0.71.1
  • CAGEfightR 1.20.0
  • CAGEr 2.6.1
  • CAMERA 1.56.0
  • Category 2.66.0
  • ccdata 1.26.0
  • ccmap 1.26.0
  • CGHbase 1.60.0
  • CGHcall 2.62.0
  • ChIPpeakAnno 3.34.1
  • chromVAR 1.22.1
  • clusterProfiler 4.8.1
  • CNEr 1.36.0
  • coloc 5.2.2
  • colorRamps 2.3.1
  • ComplexHeatmap 2.16.0
  • ConsensusClusterPlus 1.64.0
  • conumee 1.34.0
  • crossmeta 1.26.0
  • cummeRbund 2.42.0
  • cytolib 2.12.0
  • CytoML 2.12.0
  • dada2 1.28.0
  • ddPCRclust 1.20.0
  • DECIPHER 2.28.0
  • DeconRNASeq 1.42.0
  • decontam 1.20.0
  • DEGseq 1.54.0
  • DelayedArray 0.26.6
  • DelayedMatrixStats 1.22.1
  • densEstBayes-1.0-2.2
  • densvis 1.10.2
  • derfinder 1.34.0
  • derfinderHelper 1.34.0
  • DESeq2 1.40.2
  • diffcyt 1.20.0
  • dir.expiry 1.8.0
  • DirichletMultinomial 1.42.0
  • DNABarcodes 1.30.0
  • DNAcopy 1.74.1
  • DO.db 2.9
  • docopt 0.7.1
  • DOSE 3.26.1
  • dqrng 0.3.0
  • DRIMSeq 1.28.0
  • DropletUtils 1.20.0
  • DSS 2.48.0
  • dupRadar 1.30.0
  • DynDoc 1.78.0
  • EBImage 4.42.0
  • edgeR 3.42.4
  • egg 0.4.5
  • enrichplot 1.20.0
  • EnsDb.Hsapiens.v75 2.99.0
  • EnsDb.Hsapiens.v79 2.99.0
  • EnsDb.Hsapiens.v86 2.99.0
  • ensembldb 2.24.0
  • ExperimentHub 2.8.0
  • extraDistr 1.9.1
  • fda 6.1.4
  • FDb.InfiniumMethylation.hg19 2.2.0
  • fds 1.8
  • feature 1.2.15
  • fgsea 1.26.0
  • filelock 1.0.2
  • flowAI 1.30.0
  • flowClean 1.38.0
  • flowClust 3.38.0
  • flowCore 2.12.0
  • flowDensity 1.34.0
  • flowFP 1.58.0
  • flowMerge 2.48.0
  • flowPeaks 1.46.0
  • FlowSOM 2.8.0
  • FlowSorted.Blood.EPIC 2.4.2
  • FlowSorted.CordBloodCombined.450k 1.16.0
  • flowStats 4.12.0
  • flowViz 1.64.0
  • flowWorkspace 4.12.0
  • FRASER 1.12.1
  • fresh 0.2.0
  • gcrma 2.72.0
  • gdsfmt 1.36.1
  • genefilter 1.82.1
  • geneLenDataBase 1.36.0
  • geneplotter 1.78.0
  • GENESIS 2.30.0
  • GENIE3 1.22.0
  • GenomeInfoDb 1.36.1
  • GenomeInfoDbData 1.2.10
  • GenomicAlignments 1.36.0
  • GenomicFeatures 1.52.1
  • GenomicFiles 1.36.0
  • GenomicInteractions 1.34.0
  • GenomicRanges 1.52.0
  • GenomicScores 2.12.0
  • GEOmap-2.5-0
  • GEOquery 2.68.0
  • ggbio 1.48.0
  • ggcyto 1.28.0
  • ggdendro 0.1.23
  • ggnewscale 0.4.9
  • ggpointdensity 0.1.0
  • ggrastr 1.0.2
  • ggseqlogo 0.1
  • ggthemes 4.2.4
  • ggtree 3.8.0
  • GLAD 2.64.0
  • Glimma 2.10.0
  • GlobalAncova 4.18.0
  • globaltest 5.54.0
  • GO.db 3.17.0
  • GOSemSim 2.26.0
  • goseq 1.52.0
  • GOstats 2.66.0
  • graph 1.78.0
  • graphite 1.46.0
  • GSEABase 1.62.0
  • gsmoothr 0.1.7
  • gson 0.1.0
  • GSVA 1.48.2
  • Gviz 1.44.0
  • GWASExactHW 1.01
  • GWASTools 1.46.0
  • HDF5Array 1.28.1
  • HDO.db 0.99.1
  • hdrcde 3.4
  • heatmaply 1.4.2
  • hgu133plus2.db 3.13.0
  • HiCBricks 1.18.0
  • HiCcompare 1.22.1
  • HMMcopy 1.42.0
  • Homo.sapiens 1.3.1
  • IHW 1.28.0
  • 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 0.42.0
  • impute 1.74.1
  • InteractionSet 1.28.1
  • interactiveDisplayBase 1.38.0
  • IRanges 2.34.1
  • isva 1.9
  • JASPAR2020 0.99.10
  • KEGGgraph 1.60.0
  • KEGGREST 1.40.0
  • LEA 3.12.2
  • limma 3.56.2
  • lpsymphony 1.28.1
  • lsa 0.73.3
  • lumi 2.52.0
  • M3Drop 1.26.0
  • marray 1.78.0
  • maSigPro 1.72.0
  • MassSpecWavelet 1.66.0
  • MatrixGenerics 1.12.2
  • MBA-0.1-0
  • MEDIPS 1.52.0
  • metagenomeSeq 1.42.0
  • metaMA 3.1.3
  • metap 1.8
  • metapod 1.8.0
  • MethylSeekR 1.40.0
  • methylumi 2.46.0
  • Mfuzz 2.60.0
  • mia 1.8.0
  • minfi 1.46.0
  • missMethyl 1.34.0
  • mixOmics 6.24.0
  • mixsqp-0.3-48
  • MLInterfaces 1.80.0
  • MotifDb 1.42.0
  • motifmatchr 1.22.0
  • motifStack 1.44.1
  • MsCoreUtils 1.12.0
  • MsFeatures 1.8.0
  • MSnbase 2.26.0
  • MultiAssayExperiment 1.26.0
  • MultiDataSet 1.28.0
  • multtest 2.56.0
  • muscat 1.14.0
  • mutoss-0.1-13
  • mzID 1.38.0
  • mzR 2.34.1
  • NADA-1.6-1.1
  • ncdfFlow 2.46.0
  • NMF 0.26
  • NOISeq 2.44.0
  • numbat-1.3.2-1
  • oligo 1.64.1
  • oligoClasses 1.62.0
  • ontologyIndex 2.11
  • openCyto 2.12.0
  • org.Hs.eg.db 3.17.0
  • org.Mm.eg.db 3.17.0
  • org.Rn.eg.db 3.17.0
  • OrganismDbi 1.42.0
  • OUTRIDER 1.18.1
  • pathview 1.40.0
  • pcaMethods 1.92.0
  • perm-1.0-0.2
  • PFAM.db 3.17.0
  • phyloseq 1.44.0
  • pmp 1.12.0
  • polyester 1.36.0
  • poweRlaw 0.70.6
  • preprocessCore 1.62.1
  • pRoloc 1.40.1
  • pRolocdata 1.38.0
  • pRolocGUI 2.10.0
  • ProtGenerics 1.32.0
  • PRROC 1.3.1
  • PSCBS 0.66.0
  • PureCN 2.6.4
  • qap-0.1-2
  • QDNAseq 1.36.0
  • qlcMatrix 0.9.7
  • qqconf 1.3.2
  • quantsmooth 1.66.0
  • qvalue 2.32.0
  • R.devices 2.17.1
  • R.filesets 2.15.0
  • R.huge 0.10.0
  • rainbow 3.7
  • randomcoloR 1.1.0.1
  • RBGL 1.76.0
  • RcisTarget 1.20.0
  • RcppAnnoy 0.0.21
  • RcppHNSW 0.4.1
  • RcppML 0.3.7
  • RcppZiggurat 0.1.6
  • reactome.db 1.84.0
  • ReactomePA 1.44.0
  • regioneR 1.32.0
  • reldist-1.7-2
  • remaCor 0.0.16
  • Repitools 1.46.0
  • ReportingTools 2.39.0
  • ResidualMatrix 1.10.0
  • restfulr 0.0.15
  • Rfast 2.0.8
  • RFOC-3.4-6
  • rGADEM 2.48.0
  • Rgraphviz 2.44.0
  • rhdf5 2.44.0
  • rhdf5filters 1.12.1
  • Rhdf5lib 1.22.0
  • Rhtslib 2.2.0
  • Ringo 1.64.0
  • RNASeqPower 1.40.0
  • ROC 1.76.0
  • rols 2.28.0
  • ROntoTools 2.28.0
  • ropls 1.32.0
  • RPMG-2.2-3
  • RProtoBufLib 2.12.0
  • Rsamtools 2.16.0
  • RSEIS-4.1-4
  • Rsubread 2.14.2
  • rsvd 1.0.5
  • rtracklayer 1.60.0
  • Rwave-2.6-5
  • S4Arrays 1.0.4
  • S4Vectors 0.38.1
  • samr 3.0
  • SamSPECTRAL 1.54.0
  • SC3 1.28.3
  • ScaledMatrix 1.8.1
  • SCANVIS 1.14.0
  • scater 1.28.0
  • scattermore 1.2
  • scDblFinder 1.14.0
  • scistreer 1.2.0
  • scran 1.28.1
  • scrime 1.3.5
  • scuttle 1.10.1
  • SeqArray 1.40.1
  • seqLogo 1.66.0
  • SeqVarTools 1.38.0
  • seriation 1.4.2
  • Seurat 4.3.0.1
  • SeuratObject 4.1.3
  • shinyBS 0.61.1
  • shinydashboardPlus 2.0.3
  • shinyFiles 0.9.3
  • shinyhelper 0.3.2
  • shinypanel 0.1.5
  • shinyWidgets 0.7.6
  • ShortRead 1.58.0
  • siggenes 1.74.0
  • Signac 1.10.0
  • simplifyEnrichment 1.10.0
  • SingleCellExperiment 1.22.0
  • SingleR 2.2.0
  • sitmo 2.0.2
  • slingshot 2.8.0
  • SMVar 1.3.4
  • SNPRelate 1.34.1
  • snpStats 1.50.0
  • sparseMatrixStats 1.12.2
  • sparsesvd-0.2-2
  • SpatialExperiment 1.10.0
  • SPIA 2.52.0
  • splancs-2.01-43
  • SPOTlight 1.4.1
  • stageR 1.22.0
  • struct 1.12.0
  • structToolbox 1.12.0
  • SummarizedExperiment 1.30.2
  • susieR 0.12.35
  • sva 3.48.0
  • TFBSTools 1.38.0
  • TFMPvalue 0.0.9
  • tkWidgets 1.78.0
  • TrajectoryUtils 1.8.0
  • treeio 1.24.1
  • TreeSummarizedExperiment 2.8.0
  • TSP-1.2-4
  • TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
  • TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
  • tximport 1.28.0
  • UCell 2.4.0
  • uwot 0.1.16
  • variancePartition 1.30.2
  • VariantAnnotation 1.46.0
  • venn 1.11
  • vsn 3.68.0
  • waiter 0.2.5
  • wateRmelon 2.6.0
  • WGCNA-1.72-1
  • widgetTools 1.78.0
  • Wrench 1.18.0
  • xcms 3.22.0
  • XVector 0.40.0
  • zCompositions-1.4.0-1
  • zellkonverter 1.10.1
  • zlibbioc 1.46.0

More Information

For more information visit the R-bundle-Bioconductor website.

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: arrow-R/11.0.0.3-foss-2022b-R-4.3.1 Boost/1.81.0-GCC-12.2.0 foss/2022b GSL/2.7-GCCcore-12.2.0 HDF5/1.14.0-gompi-2022b R/4.3.1-foss-2022b

Required By

This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2022b-foss-2022b-R-4.3.1 celldex/1.10.1-foss-2022b-R-4.3.1 faahKO/1.40.0-foss-2022b-R-4.3.1 maftools/2.16.0-foss-2022b-R-4.3.1 MAST/1.26.0-foss-2022b-R-4.3.1 MOFA2/1.10.0-foss-2022b-R-4.3.1 monocle/2.28.0-foss-2022b-R-4.3.1 msPurity/1.26.0-foss-2022b-R-4.3.1 MSstats/4.8.6-foss-2022b-R-4.3.1 pandaR/1.32.0-foss-2022b-R-4.3.1 sequenza/3.0.0-foss-2022b

Other Versions

These versions of R-bundle-Bioconductor are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 19th July 2023