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

There is a newer install 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

2020b

Architectures

EL8-cascadelake

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

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