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

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, BEAR Cloud VMs, and CaStLeS VMs):

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

BEAR Apps Version

2019b

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 PAIRADISE/1.6.0-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/1.2.1-foss-2020b-R-4.0.3-Seurat-af2925c Signac/1.3.0-foss-2020b-R-4.0.3 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, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 23rd February 2021