R-bundle-Bioconductor 3.12-foss-2020b-R-4.0.3

Deprecated: Use of this version of R-bundle-Bioconductor is deprecated. More information on our Applications Support and Retention Policy.

There is a newer version of R-bundle-Bioconductor

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

Accessing R-bundle-Bioconductor 3.12-foss-2020b-R-4.0.3

To load the module for R-bundle-Bioconductor 3.12-foss-2020b-R-4.0.3 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load R-bundle-Bioconductor/3.12-foss-2020b-R-4.0.3

BEAR Apps Version

2018b

Extensions

  • admisc 0.11
  • affxparser 1.62.0
  • affy 1.68.0
  • affycoretools 1.62.0
  • affyio 1.60.0
  • AgiMicroRna 2.40.0
  • agricolae-1.3-3
  • ALDEx2 1.22.0
  • ALL 1.32.0
  • annaffy 1.62.0
  • annotate 1.68.0
  • AnnotationDbi 1.52.0
  • AnnotationFilter 1.14.0
  • AnnotationForge 1.32.0
  • AnnotationHub 2.22.0
  • aroma.affymetrix 3.2.0
  • aroma.apd 0.6.0
  • aroma.core 3.2.2
  • aroma.light 3.20.0
  • ash-1.0-15
  • ATACseqQC 1.14.4
  • aws.s3 0.3.21
  • aws.signature 0.6.0
  • ballgown 2.22.0
  • batchelor 1.6.2
  • baySeq 2.24.0
  • beachmat 2.6.4
  • BH-1.75.0-0
  • Biobase 2.50.0
  • BiocFileCache 1.14.0
  • BiocGenerics 0.36.0
  • BiocManager 1.30.10
  • BiocNeighbors 1.8.2
  • BiocParallel 1.24.1
  • BiocSingular 1.6.0
  • BiocStyle 2.18.1
  • BiocVersion 3.12.0
  • biomaRt 2.46.3
  • biomformat 1.18.0
  • Biostrings 2.58.0
  • biovizBase 1.38.0
  • blme-1.0-5
  • bluster 1.0.0
  • bookdown 0.21
  • BSgenome 1.58.0
  • 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 1.32.0
  • CAMERA 1.46.0
  • Category 2.56.0
  • ccdata 1.16.0
  • ccmap 1.16.0
  • CGHbase 1.50.0
  • ChIPpeakAnno 3.24.1
  • coloc-3.2-1
  • colorRamps 2.3
  • ComplexHeatmap 2.6.2
  • ConsensusClusterPlus 1.54.0
  • conumee 1.24.0
  • crossmeta 1.16.1
  • cummeRbund 2.32.0
  • cytolib 2.2.1
  • CytoML 2.2.1
  • dada2 1.18.0
  • DeconRNASeq 1.32.0
  • DEGseq 1.44.0
  • DelayedArray 0.16.1
  • DelayedMatrixStats 1.12.3
  • derfinder 1.24.2
  • derfinderHelper 1.24.1
  • DESeq2 1.30.0
  • diffcyt 1.10.0
  • DNAcopy 1.64.0
  • dqrng 0.2.1
  • DRIMSeq 1.18.0
  • DropletUtils 1.10.3
  • dupRadar 1.20.0
  • DynDoc 1.68.0
  • EBImage 4.32.0
  • edgeR 3.32.1
  • emmeans 1.5.4
  • EnsDb.Hsapiens.v75 2.99.0
  • EnsDb.Hsapiens.v86 2.99.0
  • ensembldb 2.14.0
  • estimability 1.3
  • ExperimentHub 1.16.0
  • fda 5.1.9
  • FDb.InfiniumMethylation.hg19 2.2.0
  • fds 1.8
  • fgsea 1.16.0
  • flowClust 3.28.0
  • flowCore 2.2.0
  • FlowSOM 1.22.0
  • FlowSorted.Blood.EPIC 1.8.0
  • FlowSorted.CordBloodCombined.450k 1.6.0
  • flowStats 4.2.0
  • flowViz 1.54.0
  • flowWorkspace 4.2.0
  • gcrma 2.62.0
  • gdsfmt 1.26.1
  • genefilter 1.72.1
  • geneLenDataBase 1.26.0
  • geneplotter 1.68.0
  • GENESIS 2.20.1
  • GENIE3 1.12.0
  • GenomeInfoDb 1.26.2
  • GenomeInfoDbData 1.2.4
  • GenomicAlignments 1.26.0
  • GenomicFeatures 1.42.1
  • GenomicFiles 1.26.0
  • GenomicRanges 1.42.0
  • GenomicScores 2.2.0
  • genoset 1.45.1
  • GEOquery 2.58.0
  • ggbio 1.38.0
  • ggcyto 1.18.0
  • ggdendro 0.1.22
  • ggseqlogo 0.1
  • ggthemes 4.2.4
  • GLAD 2.54.0
  • Glimma 2.0.0
  • GlobalAncova 4.8.0
  • globaltest 5.44.0
  • GO.db 3.12.1
  • goseq 1.42.0
  • GOstats 2.56.0
  • graph 1.68.0
  • GSEABase 1.52.1
  • gsmoothr 0.1.7
  • GSVA 1.38.2
  • Gviz 1.34.0
  • GWASExactHW 1.01
  • GWASTools 1.36.0
  • HDF5Array 1.18.1
  • hdrcde 3.4
  • hgu133plus2.db 3.2.3
  • HMMcopy 1.32.0
  • Homo.sapiens 1.3.1
  • IHW 1.18.0
  • 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 0.32.0
  • impute 1.64.0
  • interactiveDisplayBase 1.28.0
  • IRanges 2.24.1
  • isva 1.9
  • KEGG.db 3.2.4
  • KEGGgraph 1.50.0
  • KEGGprofile 1.32.0
  • KEGGREST 1.30.1
  • LEA 3.2.0
  • limma 3.46.0
  • lpsymphony 1.18.0
  • lsa 0.73.2
  • lumi 2.42.0
  • marray 1.68.0
  • maSigPro 1.62.0
  • MassSpecWavelet 1.56.0
  • mathjaxr-1.2-0
  • MatrixGenerics 1.2.0
  • MEDIPS 1.42.0
  • metagenomeSeq 1.32.0
  • metaMA 3.1.2
  • metap 1.4
  • MethylSeekR 1.30.0
  • methylumi 2.36.0
  • Mfuzz 2.50.0
  • minfi 1.36.0
  • missMethyl 1.24.0
  • mixOmics 6.14.0
  • MLInterfaces 1.70.0
  • MotifDb 1.32.0
  • motifStack 1.34.0
  • MsCoreUtils 1.2.0
  • MSnbase 2.16.1
  • MultiDataSet 1.18.1
  • multtest 2.46.0
  • muscat 1.4.0
  • mutoss-0.1-12
  • mzID 1.28.0
  • mzR 2.24.1
  • NADA-1.6-1.1
  • ncdf4 1.17
  • ncdfFlow 2.36.0
  • NOISeq 2.34.0
  • oligo 1.54.1
  • oligoClasses 1.52.0
  • ontologyIndex 2.7
  • openCyto 2.2.0
  • org.Hs.eg.db 3.12.0
  • org.Mm.eg.db 3.12.0
  • org.Rn.eg.db 3.12.0
  • OrganismDbi 1.32.0
  • pcaMethods 1.82.0
  • perm-1.0-0.0
  • PFAM.db 3.12.0
  • phyloseq 1.34.0
  • pmp 1.2.0
  • polyester 1.26.0
  • preprocessCore 1.52.1
  • pRoloc 1.30.0
  • pRolocdata 1.28.0
  • pRolocGUI 2.0.0
  • ProtGenerics 1.22.0
  • PSCBS 0.65.0
  • PureCN 1.20.0
  • quantsmooth 1.56.0
  • qvalue 2.22.0
  • 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 1.66.0
  • RcppAnnoy 0.0.18
  • RcppHNSW 0.3.0
  • RcppZiggurat 0.1.6
  • regioneR 1.22.0
  • Repitools 1.36.0
  • ReportingTools 2.30.0
  • ResidualMatrix 1.0.0
  • Rfast 2.0.1
  • rGADEM 2.38.0
  • Rgraphviz 2.34.0
  • rhdf5 2.34.0
  • rhdf5filters 1.2.0
  • Rhdf5lib 1.12.1
  • Rhtslib 1.22.0
  • Ringo 1.54.0
  • RNASeqPower 1.30.0
  • ROC 1.66.0
  • ropls 1.22.0
  • RProtoBufLib 2.2.0
  • Rsamtools 2.6.0
  • Rsolnp 1.16
  • RSpectra-0.16-0
  • Rsubread 2.4.2
  • rsvd 1.0.3
  • rtracklayer 1.50.0
  • S4Vectors 0.28.1
  • samr 3.0
  • SC3 1.18.0
  • SCANVIS 1.4.0
  • scater 1.18.3
  • scattermore 0.7
  • scran 1.18.5
  • scrime 1.3.5
  • sctransform 0.3.2
  • scuttle 1.0.4
  • SeqArray 1.30.0
  • seqLogo 1.56.0
  • SeqVarTools 1.28.1
  • Seurat 4.0.0
  • SeuratObject 4.0.0
  • shinyBS 0.61
  • shinydashboardPlus 0.7.5
  • shinyFiles 0.9.0
  • shinyhelper 0.3.2
  • shinypanel 0.1.4
  • shinyWidgets 0.5.7
  • ShortRead 1.48.0
  • siggenes 1.64.0
  • Signac 1.1.1
  • SingleCellExperiment 1.12.0
  • SingleR 1.4.1
  • sitmo 2.0.1
  • SMVar 1.3.3
  • SNPRelate 1.24.0
  • snpStats 1.40.0
  • sparseMatrixStats 1.2.1
  • SPIA 2.42.0
  • SSPA 2.30.0
  • stageR 1.12.0
  • struct 1.2.0
  • structToolbox 1.2.0
  • SummarizedExperiment 1.20.0
  • sva 3.38.0
  • tkWidgets 1.68.0
  • truncnorm-1.0-8
  • TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
  • TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
  • tximport 1.18.0
  • uwot 0.1.10
  • variancePartition 1.20.0
  • VariantAnnotation 1.36.0
  • venn 1.9
  • vsn 3.58.0
  • wateRmelon 1.34.0
  • widgetTools 1.68.0
  • Wrench 1.8.0
  • xcms 3.12.0
  • xgboost 1.3.2.1
  • XVector 0.30.0
  • zCompositions 1.3.4
  • zlibbioc 1.36.0

More Information

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

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: Boost/1.74.0-GCC-10.2.0 foss/2020b GSL/2.6-GCC-10.2.0 HDF5/1.10.7-gompi-2020b ncdf4/1.17-foss-2020b-R-4.0.3 R/4.0.3-foss-2020b

Required By

This version of R-bundle-Bioconductor is a direct dependent of: ABSOLUTE/1.0.6-foss-2020b-R-4.0.3 BEAR-R-bio/2020b-foss-2020b-R-4.0.3 clusterProfiler/3.16.1-foss-2020b-R-4.0.3 flowVS/1.22.4-foss-2020b-R-4.0.3 harmony/1.0.0-20201009-foss-2020b-R-4.0.3 IPO/1.16.0-foss-2020b JASPAR2020/0.99.10-foss-2020b-R-4.0.3 MOFA2/1.0.1-foss-2020b-R-4.0.3 Monocle3/1.0.0-foss-2020b-R-4.0.3 motifmatchr/1.12.0-foss-2020b-R-4.0.3 Seurat/4.0.4-foss-2020b-R-4.0.3 Seurat/af2925c-foss-2020b-R-4.0.3 SeuratWrappers/20210730-foss-2020b-R-4.0.3 Signac/1.3.0-foss-2020b-R-4.0.3 Signac/1.2.1-foss-2020b-R-4.0.3-Seurat-af2925c SingCellaR/1.2.0-foss-2020b-R-4.0.3 TFBSTools/1.28.0-foss-2020b-R-4.0.3

Other Versions

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

Last modified on 23rd February 2021