R-bundle-Bioconductor 3.11-foss-2020a-R-4.0.0

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

Accessing R-bundle-Bioconductor 3.11-foss-2020a-R-4.0.0

To load the module for R-bundle-Bioconductor 3.11-foss-2020a-R-4.0.0 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/3.11-foss-2020a-R-4.0.0

BEAR Apps Version

2019h

Extensions

  • admisc 0.8
  • affy 1.66.0
  • affycoretools 1.60.0
  • affyio 1.58.0
  • AgiMicroRna 2.38.0
  • ALDEx2 1.20.0
  • ALL 1.30.0
  • annaffy 1.60.0
  • annotate 1.66.0
  • AnnotationDbi 1.50.0
  • AnnotationFilter 1.12.0
  • AnnotationForge 1.30.1
  • AnnotationHub 2.20.0
  • aroma.affymetrix 3.2.0
  • aroma.apd 0.6.0
  • aroma.core 3.2.1
  • aroma.light 3.18.0
  • askpass 1.1
  • ATACseqQC 1.12.0
  • ballgown 2.20.0
  • batchelor 1.4.0
  • baySeq 2.22.0
  • beachmat 2.4.0
  • Biobase 2.48.0
  • BiocFileCache 1.12.0
  • BiocGenerics 0.34.0
  • BiocManager 1.30.10
  • BiocNeighbors 1.6.0
  • BiocParallel 1.22.0
  • BiocSingular 1.4.0
  • BiocVersion 3.11.1
  • biomaRt 2.44.0
  • biomformat 1.16.0
  • Biostrings 2.56.0
  • biovizBase 1.36.0
  • blme-1.0-4
  • BSgenome 1.56.0
  • BSgenome.Hsapiens.UCSC.hg19 1.4.3
  • BSgenome.Hsapiens.UCSC.hg38 1.4.3
  • BSgenome.Mmusculus.UCSC.mm10 1.4.0
  • bumphunter 1.30.0
  • CAMERA 1.44.0
  • Category 2.54.0
  • CGHbase 1.48.0
  • ChIPpeakAnno 3.22.0
  • clue-0.3-57
  • colorRamps 2.3
  • ComplexHeatmap 2.4.2
  • ConsensusClusterPlus 1.52.0
  • conumee 1.22.0
  • cummeRbund 2.30.0
  • cytolib 2.0.0
  • CytoML 2.0.0
  • dada2 1.16.0
  • DeconRNASeq 1.30.0
  • DEGseq 1.42.0
  • DelayedArray 0.14.0
  • DelayedMatrixStats 1.10.0
  • derfinder 1.22.0
  • derfinderHelper 1.22.0
  • DESeq2 1.28.0
  • diffcyt 1.8.0
  • DNAcopy 1.62.0
  • dqrng 0.2.1
  • DropletUtils 1.8.0
  • dupRadar 1.18.0
  • DynDoc 1.66.0
  • EBImage 4.30.0
  • edgeR 3.30.0
  • ensembldb 2.12.0
  • fda 5.1.4
  • FDb.InfiniumMethylation.hg19 2.2.0
  • fgsea 1.14.0
  • flowClust 3.26.0
  • flowCore 2.0.0
  • FlowSOM 1.20.0
  • flowStats 4.0.0
  • flowViz 1.52.0
  • flowWorkspace 4.0.0
  • fs 1.4.1
  • gcrma 2.60.0
  • gdsfmt 1.24.0
  • genefilter 1.70.0
  • geneLenDataBase 1.24.0
  • geneplotter 1.66.0
  • GENESIS 2.18.0
  • GENIE3 1.10.0
  • GenomeInfoDb 1.24.0
  • GenomeInfoDbData 1.2.3
  • GenomicAlignments 1.24.0
  • GenomicFeatures 1.40.0
  • GenomicFiles 1.24.0
  • GenomicRanges 1.40.0
  • GenomicScores 2.0.0
  • genoset 1.44.0
  • GEOquery 2.56.0
  • ggbio 1.36.0
  • ggcyto 1.16.0
  • ggplot2 3.3.0
  • Glimma 1.16.0
  • GlobalAncova 4.6.0
  • globaltest 5.42.0
  • GO.db 3.11.1
  • goseq 1.40.0
  • GOstats 2.54.0
  • graph 1.66.0
  • GSEABase 1.50.0
  • gsmoothr 0.1.7
  • GSVA 1.36.0
  • Gviz 1.32.0
  • GWASExactHW 1.01
  • GWASTools 1.34.0
  • HDF5Array 1.16.0
  • hgu133plus2.db 3.2.3
  • HMMcopy 1.30.0
  • Homo.sapiens 1.3.1
  • IHW 1.16.0
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0
  • IlluminaHumanMethylation450kmanifest 0.4.0
  • IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
  • IlluminaHumanMethylationEPICmanifest 0.3.0
  • illuminaio 0.30.0
  • impute 1.62.0
  • interactiveDisplayBase 1.26.0
  • IRanges 2.22.1
  • isoband 0.2.1
  • KEGG.db 3.2.4
  • KEGGgraph 1.48.0
  • KEGGprofile 1.30.0
  • KEGGREST 1.28.0
  • LEA 3.0.0
  • limma 3.44.1
  • lpsymphony 1.16.0
  • lumi 2.40.0
  • MALDIquant 1.19.3
  • marray 1.66.0
  • maSigPro 1.60.0
  • MassSpecWavelet 1.54.0
  • MEDIPS 1.40.0
  • metagenomeSeq 1.30.0
  • metap 1.3
  • methylumi 2.34.0
  • Mfuzz 2.48.0
  • minfi 1.34.0
  • mixOmics 6.12.0
  • MLInterfaces 1.68.0
  • MotifDb 1.30.0
  • motifStack 1.32.0
  • MotIV 1.43.0
  • MSnbase 2.14.0
  • multtest 2.44.0
  • muscat 1.2.0
  • mutoss-0.1-12
  • mzID 1.26.0
  • mzR 2.22.0
  • NADA-1.6-1.1
  • ncdfFlow 2.34.0
  • NOISeq 2.31.0
  • oligoClasses 1.50.0
  • openCyto 2.0.0
  • org.Hs.eg.db 3.11.1
  • OrganismDbi 1.30.0
  • pcaMethods 1.80.0
  • perm-1.0-0.0
  • PFAM.db 3.11.1
  • phyloseq 1.32.0
  • polyester 1.24.0
  • preprocessCore 1.50.0
  • pRoloc 1.28.0
  • pRolocdata 1.26.0
  • pRolocGUI 1.22.0
  • ProtGenerics 1.20.0
  • PSCBS 0.65.0
  • PureCN 1.18.0
  • quantsmooth 1.54.0
  • qvalue 2.20.0
  • R.devices 2.16.1
  • R.filesets 2.13.0
  • R.huge 0.9.0
  • R.utils 2.9.2
  • rappdirs 0.3.1
  • rARPACK-0.11-0
  • RBGL 1.64.0
  • RcppAnnoy 0.0.16
  • RcppHNSW 0.2.0
  • RcppParallel 5.0.1
  • RcppZiggurat 0.1.5
  • readr 1.3.1
  • regioneR 1.20.0
  • Repitools 1.34.0
  • ReportingTools 2.28.0
  • Rfast 1.9.9
  • rGADEM 2.36.0
  • Rgraphviz 2.32.0
  • rhdf5 2.32.0
  • Rhdf5lib 1.10.0
  • Rhtslib 1.20.0
  • Ringo 1.52.0
  • RNASeqPower 1.28.0
  • RProtoBufLib 2.0.0
  • RProtoBufLib 2.0.0
  • Rsamtools 2.4.0
  • Rsolnp 1.16
  • RSpectra-0.16-0
  • Rsubread 2.2.1
  • rsvd 1.0.3
  • rtracklayer 1.48.0
  • S4Vectors 0.26.0
  • samr 3.0
  • SC3 1.16.0
  • scater 1.16.0
  • scran 1.16.0
  • scrime 1.3.5
  • SeqArray 1.28.0
  • seqLogo 1.54.1
  • SeqVarTools 1.26.0
  • Seurat 3.1.5
  • shinyFiles 0.8.0
  • ShortRead 1.46.0
  • sigaR 1.35.0
  • siggenes 1.62.0
  • SingleCellExperiment 1.10.1
  • sitmo 2.0.1
  • SNPRelate 1.22.0
  • SPIA 2.40.0
  • SSPA 2.28.0
  • SummarizedExperiment 1.18.1
  • sva 3.36.0
  • sys 3.3
  • tkWidgets 1.66.0
  • truncnorm-1.0-8
  • truncnorm-1.0-8
  • TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
  • TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
  • tximport 1.16.0
  • uwot 0.1.8
  • variancePartition 1.18.0
  • VariantAnnotation 1.34.0
  • venn 1.9
  • vsn 3.56.0
  • widgetTools 1.66.0
  • Wrench 1.6.0
  • xcms 3.10.0
  • XVector 0.28.0
  • zCompositions 1.3.4
  • zlibbioc 1.34.0

More Information

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

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: foss/2020a HDF5/1.10.6-gompi-2020a MariaDB-connector-c/3.1.7-GCCcore-9.3.0 ncdf4/1.17-foss-2020a-R-4.0.0 R/4.0.0-foss-2020a

Required By

This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2020a-foss-2020a-R-4.0.0 Cardinal/2.6.0-foss-2020a-R-4.0.0 CellChat/20210814-foss-2020a-R-4.0.0 ChAMP/2.18.3-foss-2020a-R-4.0.0 CNVkit/0.9.8-foss-2020a-Python-3.8.2-R-4.0.0 DirichletMultinomial/1.32.0-foss-2020a-R-4.0.0 DivNet/31e04e2-foss-2020a-R-4.0.0 DROP/1.0.3-foss-2020a-Python-3.8.2-R-4.0.0 EnhancedVolcano/1.6.0-foss-2020a-R-4.0.0 faahKO/1.28.0-foss-2020a-R-4.0.0 HOMER/4.11-foss-2020a MAST/1.14.0-foss-2020a-R-4.0.0 RAPID/fcd9e9b-foss-2020a-R-4.0.0 RcisTarget/1.8.0-foss-2020a-R-4.0.0 sequenza/3.0.0-foss-2020a-R-4.0.0 Seurat/4.0.0-foss-2020a-R-4.0.0 slingshot/1.6.1-foss-2020a-R-4.0.0 SRAdb/1.50.0-foss-2020a-R-4.0.0 structToolbox/1.0.1-foss-2020a-R-4.0.0 WGCNA/1.70-3-foss-2020a-R-4.0.0

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 29th May 2020