R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0

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

Accessing R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0

To load the module for R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0 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/3.13-foss-2021a-R-4.1.0

BEAR Apps Version

2019h

Extensions

  • admisc 0.15
  • affxparser 1.64.0
  • affy 1.70.0
  • affycoretools 1.64.0
  • affyio 1.62.0
  • AgiMicroRna 2.42.0
  • agricolae-1.3-3
  • ALDEx2 1.24.0
  • ALL 1.34.0
  • annaffy 1.63.1
  • annotate 1.70.0
  • AnnotationDbi 1.54.0
  • AnnotationFilter 1.16.0
  • AnnotationForge 1.34.0
  • AnnotationHub 3.0.0
  • aroma.affymetrix 3.2.0
  • aroma.apd 0.6.0
  • aroma.core 3.2.2
  • aroma.light 3.22.0
  • ash-1.0-15
  • ATACseqQC 1.16.0
  • aws.s3 0.3.21
  • aws.signature 0.6.0
  • ballgown 2.24.0
  • batchelor 1.8.0
  • baySeq 2.26.0
  • beachmat 2.8.0
  • Biobase 2.52.0
  • BiocFileCache 2.0.0
  • BiocGenerics 0.38.0
  • BiocIO 1.2.0
  • BiocManager 1.30.15
  • BiocNeighbors 1.10.0
  • BiocParallel 1.26.0
  • BiocSingular 1.8.0
  • BiocStyle 2.20.0
  • BiocVersion 3.13.1
  • biomaRt 2.48.0
  • biomformat 1.20.0
  • Biostrings 2.60.0
  • biovizBase 1.40.0
  • blme-1.0-5
  • bluster 1.2.1
  • bookdown 0.22
  • BSgenome 1.60.0
  • BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0
  • BSgenome.Hsapiens.UCSC.hg19 1.4.3
  • BSgenome.Hsapiens.UCSC.hg38 1.4.3
  • BSgenome.Mmusculus.UCSC.mm10 1.4.0
  • bumphunter 1.34.0
  • CAMERA 1.48.0
  • Category 2.58.0
  • ccdata 1.18.0
  • ccmap 1.18.0
  • CGHbase 1.52.0
  • ChIPpeakAnno 3.26.0
  • CNEr 1.28.0
  • coloc-3.2-1
  • colorRamps 2.3
  • ComplexHeatmap 2.8.0
  • ConsensusClusterPlus 1.56.0
  • conumee 1.26.0
  • crossmeta 1.18.0
  • cummeRbund 2.34.0
  • cytolib 2.4.0
  • CytoML 2.4.0
  • dada2 1.20.0
  • DeconRNASeq 1.34.0
  • DEGseq 1.46.0
  • DelayedArray 0.18.0
  • DelayedMatrixStats 1.14.0
  • derfinder 1.26.0
  • derfinderHelper 1.26.0
  • DESeq2 1.32.0
  • diffcyt 1.12.0
  • DirichletMultinomial 1.34.0
  • DNAcopy 1.66.0
  • docopt 0.7.1
  • dqrng 0.3.0
  • DRIMSeq 1.20.0
  • DropletUtils 1.12.1
  • dupRadar 1.22.0
  • DynDoc 1.70.0
  • EBImage 4.34.0
  • edgeR 3.34.0
  • egg 0.4.5
  • emmeans 1.6.1
  • EnsDb.Hsapiens.v75 2.99.0
  • EnsDb.Hsapiens.v86 2.99.0
  • ensembldb 2.16.0
  • estimability 1.3
  • ExperimentHub 2.0.0
  • extraDistr 1.9.1
  • fda 5.1.9
  • FDb.InfiniumMethylation.hg19 2.2.0
  • fds 1.8
  • fgsea 1.18.0
  • filelock 1.0.2
  • flowClust 3.30.0
  • flowCore 2.4.0
  • FlowSOM 2.0.0
  • FlowSorted.Blood.EPIC 1.10.1
  • FlowSorted.CordBloodCombined.450k 1.8.0
  • flowStats 4.4.0
  • flowViz 1.56.0
  • flowWorkspace 4.4.0
  • FRASER 1.4.0
  • fresh 0.2.0
  • gcrma 2.64.0
  • gdsfmt 1.28.0
  • GenABEL-1.8-0
  • GenABEL.data 1.0.0
  • genefilter 1.74.0
  • geneLenDataBase 1.28.0
  • geneplotter 1.70.0
  • GENESIS 2.22.0
  • GENIE3 1.14.0
  • GenomeInfoDb 1.28.0
  • GenomeInfoDbData 1.2.6
  • GenomicAlignments 1.28.0
  • GenomicFeatures 1.44.0
  • GenomicFiles 1.28.0
  • GenomicRanges 1.44.0
  • GenomicScores 2.4.0
  • GEOquery 2.60.0
  • ggbio 1.40.0
  • ggcyto 1.20.0
  • ggdendro 0.1.22
  • ggnewscale 0.4.5
  • ggpointdensity 0.1.0
  • ggseqlogo 0.1
  • ggthemes 4.2.4
  • GLAD 2.56.0
  • Glimma 2.2.0
  • GlobalAncova 4.10.0
  • globaltest 5.46.0
  • GO.db 3.13.0
  • goseq 1.44.0
  • GOstats 2.58.0
  • graph 1.70.0
  • GSEABase 1.54.0
  • gsmoothr 0.1.7
  • GSVA 1.40.0
  • Gviz 1.36.1
  • GWASExactHW 1.01
  • GWASTools 1.38.0
  • HDF5Array 1.20.0
  • hdrcde 3.4
  • heatmaply 1.2.1
  • hgu133plus2.db 3.13.0
  • HMMcopy 1.34.0
  • Homo.sapiens 1.3.1
  • IHW 1.20.0
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0
  • IlluminaHumanMethylation450kmanifest 0.4.0
  • IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
  • IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0
  • IlluminaHumanMethylationEPICmanifest 0.3.0
  • illuminaio 0.34.0
  • impute 1.66.0
  • InteractionSet 1.20.0
  • interactiveDisplayBase 1.30.0
  • IRanges 2.26.0
  • isva 1.9
  • JASPAR2020 0.99.10
  • KEGG.db 3.2.4
  • KEGGgraph 1.52.0
  • KEGGREST 1.32.0
  • LEA 3.4.0
  • limma 3.48.0
  • lpsymphony 1.20.0
  • lsa 0.73.2
  • lumi 2.44.0
  • marray 1.70.0
  • maSigPro 1.64.0
  • MassSpecWavelet 1.58.0
  • mathjaxr-1.4-0
  • MatrixGenerics 1.4.0
  • MEDIPS 1.44.0
  • metagenomeSeq 1.34.0
  • metaMA 3.1.2
  • metap 1.4
  • metapod 1.0.0
  • MethylSeekR 1.32.0
  • methylumi 2.38.0
  • Mfuzz 2.52.0
  • minfi 1.38.0
  • missMethyl 1.26.0
  • mixOmics 6.16.0
  • MLInterfaces 1.72.0
  • MotifDb 1.34.0
  • motifmatchr 1.14.0
  • motifStack 1.36.0
  • MsCoreUtils 1.4.0
  • MSnbase 2.18.0
  • MultiDataSet 1.20.0
  • multtest 2.48.0
  • muscat 1.6.0
  • mutoss-0.1-12
  • mzID 1.30.0
  • mzR 2.26.0
  • NADA-1.6-1.1
  • ncdfFlow 2.38.0
  • NOISeq 2.36.0
  • oligo 1.56.0
  • oligoClasses 1.54.0
  • ontologyIndex 2.7
  • openCyto 2.4.0
  • org.Hs.eg.db 3.13.0
  • org.Mm.eg.db 3.13.0
  • org.Rn.eg.db 3.13.0
  • OrganismDbi 1.34.0
  • OUTRIDER 1.10.0
  • pcaMethods 1.84.0
  • perm-1.0-0.0
  • PFAM.db 3.13.0
  • phyloseq 1.36.0
  • pmp 1.4.0
  • polyester 1.28.0
  • poweRlaw 0.70.6
  • preprocessCore 1.54.0
  • pRoloc 1.32.0
  • pRolocdata 1.30.0
  • pRolocGUI 2.2.0
  • ProtGenerics 1.24.0
  • PRROC 1.3.1
  • PSCBS 0.65.0
  • PureCN 1.22.1
  • qap-0.1-1
  • qlcMatrix 0.9.7
  • quantsmooth 1.58.0
  • qvalue 2.24.0
  • R.devices 2.17.0
  • R.filesets 2.14.0
  • R.huge 0.9.0
  • rainbow 3.6
  • randomcoloR 1.1.0.1
  • rARPACK-0.11-0
  • RBGL 1.68.0
  • RcppAnnoy 0.0.18
  • RcppHNSW 0.3.0
  • RcppZiggurat 0.1.6
  • regioneR 1.24.0
  • Repitools 1.38.0
  • ReportingTools 2.32.0
  • ResidualMatrix 1.2.0
  • restfulr 0.0.13
  • Rfast 2.0.3
  • rGADEM 2.40.0
  • Rgraphviz 2.36.0
  • rhdf5 2.36.0
  • rhdf5filters 1.4.0
  • Rhdf5lib 1.14.0
  • Rhtslib 1.24.0
  • Ringo 1.56.0
  • RNASeqPower 1.32.0
  • ROC 1.68.0
  • ropls 1.24.0
  • RProtoBufLib 2.4.0
  • Rsamtools 2.8.0
  • Rsolnp 1.16
  • RSpectra-0.16-0
  • Rsubread 2.6.1
  • rsvd 1.0.5
  • rtracklayer 1.52.0
  • S4Vectors 0.30.0
  • samr 3.0
  • SC3 1.20.0
  • ScaledMatrix 1.0.0
  • SCANVIS 1.6.0
  • scater 1.20.0
  • scattermore 0.7
  • scran 1.20.1
  • scrime 1.3.5
  • sctransform 0.3.2
  • scuttle 1.2.0
  • SeqArray 1.32.0
  • seqLogo 1.58.0
  • SeqVarTools 1.30.0
  • seriation-1.2-9
  • Seurat 4.0.3
  • SeuratObject 4.0.2
  • shinyBS 0.61
  • shinydashboardPlus 2.0.1
  • shinyFiles 0.9.0
  • shinyhelper 0.3.2
  • shinypanel 0.1.4
  • shinyWidgets 0.6.0
  • ShortRead 1.50.0
  • siggenes 1.66.0
  • Signac 1.2.1
  • SingleCellExperiment 1.14.1
  • SingleR 1.6.1
  • sitmo 2.0.1
  • SMVar 1.3.3
  • SNPRelate 1.26.0
  • snpStats 1.42.0
  • sparseMatrixStats 1.4.0
  • sparsesvd 0.2
  • SPIA 2.44.0
  • stageR 1.14.0
  • struct 1.4.0
  • structToolbox 1.4.0
  • SummarizedExperiment 1.22.0
  • sva 3.40.0
  • TFBSTools 1.30.0
  • TFMPvalue 0.0.8
  • tkWidgets 1.70.0
  • truncnorm-1.0-8
  • TSP-1.1-10
  • TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
  • TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
  • tximport 1.20.0
  • uwot 0.1.10
  • variancePartition 1.22.0
  • VariantAnnotation 1.38.0
  • venn 1.10
  • vsn 3.60.0
  • waiter 0.2.1
  • wateRmelon 1.36.0
  • widgetTools 1.70.0
  • Wrench 1.10.0
  • xcms 3.14.0
  • XVector 0.32.0
  • zCompositions 1.3.4
  • zlibbioc 1.38.0

More Information

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

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: Boost/1.76.0-GCC-10.3.0 foss/2021a GSL/2.7-GCC-10.3.0 HDF5/1.10.7-gompi-2021a ncdf4/1.17-foss-2021a-R-4.1.0 R/4.1.0-foss-2021a

Required By

This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2021a-foss-2021a-R-4.1.0 CAGEr/1.34.0-foss-2021a-R-4.1.0 ChIPseeker/1.28.3-foss-2021a-R-4.1.0 GeomxTools/1.0.0-foss-2021a-R-4.1.0 gsfisher/3ad1d79-foss-2021a-R-4.1.0 iClusterPlus/1.28.0-foss-2021a PharmacoGx/2.4.0-foss-2021a phenoptrReports/0.3.0-foss-2021a-R-4.1.0 rcdk/3.6.0-foss-2021a survcomp/1.42.0-foss-2021a

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 13th September 2021