R-bundle-Bioconductor 3.9-foss-2019a-R-3.6.0

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

Accessing R-bundle-Bioconductor 3.9-foss-2019a-R-3.6.0

To load the module for R-bundle-Bioconductor 3.9-foss-2019a-R-3.6.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps-unsupported/handbuilt/2019
module load R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0

BEAR Apps Version

2019h

Extensions

  • affy 1.62.0
  • affycoretools 1.56.0
  • affyio 1.54.0
  • AgiMicroRna 2.34.0
  • ALDEx2 1.16.0
  • ALL 1.26.0
  • annaffy 1.56.0
  • annotate 1.62.0
  • AnnotationDbi 1.46.1
  • AnnotationFilter 1.8.0
  • AnnotationForge 1.26.0
  • AnnotationHub 2.16.0
  • askpass 1.1
  • ballgown 2.16.0
  • baySeq 2.18.0
  • beachmat 2.0.0
  • Biobase 2.44.0
  • BiocFileCache 1.8.0
  • BiocGenerics 0.30.0
  • BiocManager 1.30.4
  • BiocNeighbors 1.2.0
  • BiocParallel 1.18.1
  • BiocSingular 1.0.0
  • biomaRt 2.40.3
  • biomformat 1.12.0
  • Biostrings 2.52.0
  • biovizBase 1.32.0
  • BSgenome 1.52.0
  • BSgenome.Hsapiens.UCSC.hg19 1.4.0
  • bsseq 1.20.0
  • bumphunter 1.26.0
  • CAMERA 1.40.0
  • CATALYST 1.8.6
  • Category 2.50.0
  • CGHbase 1.44.0
  • ChAMP 2.14.0
  • ChAMPdata 2.16.0
  • circlize 0.4.7
  • clue-0.3-57
  • ComplexHeatmap 2.0.0
  • ConsensusClusterPlus 1.48.0
  • corrplot 0.84
  • cummeRbund 2.26.0
  • cydar 1.8.0
  • dada2 1.12.1
  • DeconRNASeq 1.26.0
  • DEGseq 1.38.0
  • DelayedArray 0.10.0
  • DelayedMatrixStats 1.6.0
  • derfinder 1.18.3
  • derfinderHelper 1.18.1
  • DESeq2 1.24.0
  • diffcyt 1.4.3
  • DMRcate 1.20.0
  • DMRcatedata 1.20.0
  • DNAcopy 1.58.0
  • dqrng 0.2.1
  • drc-3.0-1
  • DropletUtils 1.4.3
  • DSS 2.32.0
  • dupRadar 1.14.0
  • DynDoc 1.62.0
  • edgeR 3.26.6
  • ensembldb 2.8.0
  • FDb.InfiniumMethylation.hg19 2.2.0
  • FEM 3.12.0
  • fgsea 1.10.0
  • flowCore 1.50.0
  • FlowSOM 1.16.0
  • flowUtils 1.48.0
  • flowViz 1.48.0
  • fs 1.3.1
  • gcrma 2.56.0
  • gdsfmt 1.20.0
  • genefilter 1.66.0
  • geneLenDataBase 1.20.0
  • geneplotter 1.62.0
  • GENESIS 2.14.3
  • GENIE3 1.6.0
  • GenomeGraphs 1.44.0
  • GenomeInfoDb 1.20.0
  • GenomeInfoDbData 1.2.1
  • GenomicAlignments 1.20.1
  • GenomicFeatures 1.36.4
  • GenomicFiles 1.20.0
  • GenomicRanges 1.36.0
  • genoset 1.40.0
  • GEOquery 2.52.0
  • ggbio 1.32.0
  • GlobalAncova 4.2.0
  • globaltest 5.38.0
  • GO.db 3.8.2
  • goseq 1.36.0
  • GOstats 2.50.0
  • graph 1.62.0
  • GSEABase 1.46.0
  • GSVA 1.32.0
  • Gviz 1.28.0
  • GWASExactHW 1.01
  • GWASTools 1.30.0
  • HDF5Array 1.12.2
  • hgu133plus2.db 3.2.3
  • Homo.sapiens 1.3.1
  • IHW 1.12.0
  • Illumina450ProbeVariants.db 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 0.26.0
  • impute 1.58.0
  • interactiveDisplayBase 1.22.0
  • IRanges 2.18.1
  • isva 1.9
  • JADE-2.0-2
  • KEGG.db 3.2.3
  • KEGGgraph 1.44.0
  • KEGGprofile 1.26.0
  • KEGGREST 1.24.0
  • kpmt 0.1.0
  • LEA 2.6.0
  • limma 3.40.6
  • lpsymphony 1.12.0
  • lumi 2.36.0
  • MALDIquant 1.19.3
  • marray 1.62.0
  • maSigPro 1.56.0
  • MassSpecWavelet 1.50.0
  • matrixStats 0.54.0
  • metagenomeSeq 1.26.3
  • methylumi 2.30.0
  • Mfuzz 2.44.0
  • minfi 1.30.0
  • missMethyl 1.18.0
  • mixOmics 6.8.0
  • MSnbase 2.10.1
  • MSnbase 2.10.1
  • multtest 2.40.0
  • mzID 1.22.0
  • mzR 2.18.0
  • ncdfFlow 2.30.1
  • NOISeq 2.28.0
  • oligoClasses 1.46.0
  • org.Hs.eg.db 3.8.2
  • OrganismDbi 1.26.0
  • pcaMethods 1.76.0
  • perm-1.0-0.0
  • PFAM.db 3.8.2
  • phyloseq 1.28.0
  • polyester 1.20.0
  • preprocessCore 1.46.0
  • prettydoc 0.3.0
  • ProtGenerics 1.16.0
  • PureCN 1.14.1
  • quantsmooth 1.50.0
  • qvalue 2.16.0
  • rappdirs 0.3.1
  • rARPACK-0.11-0
  • RBGL 1.60.0
  • RcppAnnoy 0.0.12
  • RcppHNSW 0.1.0
  • RcppParallel 4.4.3
  • readr 1.3.1
  • ReportingTools 2.24.0
  • Rgraphviz 2.28.0
  • rhdf5 2.28.0
  • Rhdf5lib 1.6.0
  • Rhtslib 1.16.1
  • RNASeqPower 1.24.0
  • ROC 1.60.0
  • RPMM 1.25
  • Rsamtools 2.0.0
  • RSpectra-0.15-0
  • Rsubread 1.34.6
  • rsvd 1.0.2
  • rtracklayer 1.44.2
  • ruv 0.9.7.1
  • S4Vectors 0.22.0
  • samr 3.0
  • SC3 1.12.0
  • scater 1.12.2
  • scran 1.12.1
  • scrime 1.3.5
  • SeqArray 1.24.2
  • SeqVarTools 1.22.0
  • shinyBS 0.61
  • shinyFiles 0.7.3
  • shinyjs 1.0
  • ShortRead 1.42.0
  • sigaR 1.32.0
  • siggenes 1.58.0
  • SingleCellExperiment 1.6.0
  • sitmo 2.0.1
  • SNPRelate 1.18.1
  • SPIA 2.36.0
  • SSPA 2.24.0
  • SummarizedExperiment 1.14.1
  • sva 3.32.1
  • sys 3.2
  • tkWidgets 1.62.0
  • TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
  • tximport 1.12.3
  • VariantAnnotation 1.30.1
  • venn 1.7
  • vsn 3.52.0
  • wateRmelon 1.28.0
  • widgetTools 1.62.0
  • Wrench 1.2.0
  • xcms 3.6.1
  • XVector 0.24.0
  • zlibbioc 1.30.0

More Information

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

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: foss/2019a HDF5/1.10.5-gompi-2019a MariaDB-connector-c/2.3.7-GCCcore-8.2.0 ncdf4/1.16.1-foss-2019a-R-3.6.0 R/3.6.0-foss-2019a

Required By

This version of R-bundle-Bioconductor is a direct dependent of: CODEX2/20191031-foss-2019a-R-3.6.0 conumee/1.18.0-foss-2019a-R-3.6.0 destiny/2.14.0-foss-2019a-R-3.6.0 DPClust/2.2.8-foss-2019a-R-3.6.0 karyoploteR/1.10.5-foss-2019a-R-3.6.0 MAST/1.10.0-foss-2019a-R-3.6.0 QDNAseq/1.20.0-foss-2019a-R-3.6.0 WGCNA/1.69-foss-2019a-R-3.6.0

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 9th September 2019