R-bundle-Bioconductor 3.19-foss-2023a-R-4.4.1

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

Accessing R-bundle-Bioconductor 3.19-foss-2023a-R-4.4.1

To load the module for R-bundle-Bioconductor 3.19-foss-2023a-R-4.4.1 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2023a
module load R-bundle-Bioconductor/3.19-foss-2023a-R-4.4.1

BEAR Apps Version

2023a

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

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

• affxparser 1.76.0
• affy 1.82.0
• affycoretools 1.76.0
• affyio 1.74.0
• AgiMicroRna 2.54.0
• agricolae-1.3-7
• ALDEx2 1.36.0
• ALL 1.46.0
• ANCOMBC 2.6.0
• annaffy 1.76.0
• annotate 1.82.0
• AnnotationDbi 1.66.0
• AnnotationFilter 1.28.0
• AnnotationForge 1.46.0
• AnnotationHub 3.12.0
• anytime 0.3.9
• aroma.affymetrix 3.2.2
• aroma.apd 0.7.0
• aroma.core 3.3.1
• aroma.light 3.34.0
• ash-1.0-15
• ATACseqQC 1.28.0
• AUCell 1.26.0
• aws.s3 0.3.21
• aws.signature 0.6.0
• babelgene 22.9
• ballgown 2.36.0
• basilisk 1.16.0
• basilisk.utils 1.16.0
• batchelor 1.20.0
• baySeq 2.38.0
• beachmat 2.20.0
• Biobase 2.64.0
• BiocBaseUtils 1.6.0
• BiocFileCache 2.12.0
• BiocGenerics 0.50.0
• BiocIO 1.14.0
• BiocManager 1.30.23
• BiocNeighbors 1.22.0
• BiocParallel 1.38.0
• BiocSingular 1.20.0
• BiocStyle 2.32.1
• BiocVersion 3.19.1
• biomaRt 2.60.0
• biomformat 1.32.0
• Biostrings 2.72.1
• biovizBase 1.52.0
• blme-1.0-5
• bluster 1.14.0
• bookdown 0.39
• BSgenome 1.72.0
• BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0
• BSgenome.Hsapiens.UCSC.hg19 1.4.3
• BSgenome.Hsapiens.UCSC.hg38 1.4.5
• BSgenome.Mmusculus.UCSC.mm10 1.4.3
• bsseq 1.40.0
• bumphunter 1.46.0
• ca 0.71.1
• CAGEfightR 1.24.0
• CAGEr 2.10.0
• CAMERA 1.60.0
• Category 2.70.0
• ccdata 1.30.0
• ccmap 1.30.0
• CGHbase 1.64.0
• CGHcall 2.66.0
• ChIPpeakAnno 3.38.0
• chromVAR 1.26.0
• clusterProfiler 4.12.0
• CNEr 1.40.0
• coloc 5.2.3
• colorRamps 2.3.4
• ComplexHeatmap 2.20.0
• ConsensusClusterPlus 1.68.0
• conumee 1.38.0
• crossmeta 1.30.0
• cummeRbund 2.46.0
• cytolib 2.16.0
• CytoML 2.16.0
• dada2 1.32.0
• ddPCRclust 1.24.0
• DECIPHER 3.0.0
• DeconRNASeq 1.46.0
• decontam 1.24.0
• decoupleR 2.10.0
• DEGseq 1.58.0
• DelayedArray 0.30.1
• DelayedMatrixStats 1.26.0
• densEstBayes-1.0-2.2
• derfinder 1.38.0
• derfinderHelper 1.38.0
• DESeq2 1.44.0
• diffcyt 1.24.0
• dir.expiry 1.12.0
• directlabels 2024.1.21
• DirichletMultinomial 1.46.0
• DNABarcodes 1.34.0
• DNAcopy 1.78.0
• DO.db 2.9
• docopt 0.7.1
• DOSE 3.30.1
• dqrng 0.4.1
• DRIMSeq 1.32.0
• DropletUtils 1.24.0
• DSS 2.52.0
• dupRadar 1.34.0
• DynDoc 1.82.0
• EBImage 4.46.0
• edgeR 4.2.0
• egg 0.4.5
• enrichplot 1.24.0
• EnsDb.Hsapiens.v75 2.99.0
• EnsDb.Hsapiens.v79 2.99.0
• EnsDb.Hsapiens.v86 2.99.0
• ensembldb 2.28.0
• escape 2.0.0
• ExperimentHub 2.12.0
• extraDistr 1.10.0
• factoextra 1.0.7
• fANCOVA-0.6-1
• fda 6.1.8
• FDb.InfiniumMethylation.hg19 2.2.0
• fds 1.8
• feature 1.2.15
• fgsea 1.30.0
• filelock 1.0.3
• flowAI 1.34.0
• flowClean 1.42.0
• flowClust 3.42.0
• flowCore 2.16.0
• flowDensity 1.38.0
• flowFP 1.62.0
• flowMerge 2.52.0
• flowPeaks 1.50.0
• FlowSOM 2.12.0
• FlowSorted.Blood.EPIC 2.8.0
• FlowSorted.CordBloodCombined.450k 1.20.0
• flowStats 4.16.0
• flowViz 1.68.0
• flowWorkspace 4.16.0
• FRASER 2.0.0
• fresh 0.2.0
• gcrma 2.76.0
• gdsfmt 1.40.0
• genefilter 1.86.0
• geneLenDataBase 1.40.1
• geneplotter 1.82.0
• GENESIS 2.34.0
• GENIE3 1.26.0
• GenomeInfoDb 1.40.1
• GenomeInfoDbData 1.2.12
• GenomicAlignments 1.40.0
• GenomicFeatures 1.56.0
• GenomicFiles 1.40.0
• GenomicInteractions 1.38.0
• GenomicRanges 1.56.1
• GenomicScores 2.16.0
• GEOmap-2.5-5
• GEOquery 2.72.0
• ggbio 1.52.0
• ggcyto 1.32.0
• ggdendro 0.2.0
• ggnewscale 0.4.10
• ggpointdensity 0.1.0
• ggrastr 1.0.2
• ggseqlogo 0.2
• ggthemes 5.1.0
• ggtree 3.12.0
• GLAD 2.68.0
• Glimma 2.14.0
• GlobalAncova 4.22.0
• globaltest 5.58.0
• GO.db 3.19.1
• GOSemSim 2.30.0
• goseq 1.56.0
• GOstats 2.70.0
• graph 1.82.0
• graphite 1.50.0
• GSEABase 1.66.0
• gsmoothr 0.1.7
• gson 0.1.0
• GSVA 1.52.3
• Gviz 1.48.0
• GWASExactHW 1.2
• GWASTools 1.50.0
• hahmmr 1.0.0
• HDF5Array 1.32.0
• HDO.db 0.99.1
• hdrcde 3.4
• heatmaply 1.5.0
• hgu133plus2.db 3.13.0
• HiCBricks 1.22.0
• HiCcompare 1.26.0
• HMMcopy 1.46.0
• Homo.sapiens 1.3.1
• IHW 1.32.0
• IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.1
• IlluminaHumanMethylation450kmanifest 0.4.0
• IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
• IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0
• IlluminaHumanMethylationEPICmanifest 0.3.0
• illuminaio 0.46.0
• impute 1.78.0
• InteractionSet 1.32.0
• interactiveDisplayBase 1.42.0
• intervals 0.15.4
• IRanges 2.38.0
• isva 1.9
• JASPAR2020 0.99.10
• KEGGgraph 1.64.0
• KEGGREST 1.44.1
• LEA 3.16.0
• limma 3.60.3
• log4r 0.4.3
• lpsymphony 1.32.0
• lsa 0.73.3
• lumi 2.56.0
• M3Drop 1.30.0
• marray 1.82.0
• maSigPro 1.76.0
• MassSpecWavelet 1.70.0
• MatrixGenerics 1.16.0
• MBA-0.1-0
• MEDIPS 1.56.0
• MetaboCoreUtils 1.12.0
• metagenomeSeq 1.46.0
• metaMA 3.1.3
• metap 1.10
• metapod 1.12.0
• MethylSeekR 1.44.0
• methylumi 2.50.0
• Mfuzz 2.64.0
• mia 1.12.0
• minfi 1.50.0
• missMethyl 1.38.0
• mixOmics 6.28.0
• mixsqp-0.3-54
• MLInterfaces 1.84.0
• MotifDb 1.46.0
• motifmatchr 1.26.0
• motifStack 1.48.0
• MsCoreUtils 1.16.0
• MsExperiment 1.6.0
• MsFeatures 1.12.0
• msigdbr 7.5.1
• MSnbase 2.30.1
• MSstats 4.12.0
• MSstatsConvert 1.14.0
• MSstatsLiP 1.10.0
• MSstatsPTM 2.6.0
• MSstatsTMT 2.12.1
• MultiAssayExperiment 1.30.2
• MultiDataSet 1.32.0
• multtest 2.60.0
• muscat 1.18.0
• mutoss-0.1-13
• mzID 1.42.0
• mzR 2.38.0
• NADA-1.6-1.1
• ncdfFlow 2.50.0
• NMF 0.27
• NOISeq 2.48.0
• numbat 1.4.0
• oligo 1.68.2
• oligoClasses 1.66.0
• ontologyIndex 2.12
• oompaBase 3.2.9
• oompaData 3.1.4
• openCyto 2.16.1
• org.Hs.eg.db 3.19.1
• org.Mm.eg.db 3.19.1
• org.Rn.eg.db 3.19.1
• OrganismDbi 1.46.0
• OUTRIDER 1.22.0
• pathview 1.44.0
• pcaMethods 1.96.0
• perm-1.0-0.4
• PFAM.db 3.19.1
• phyloseq 1.48.0
• plyranges 1.24.0
• pmp 1.16.0
• polyester 1.39.0
• poweRlaw 0.80.0
• preprocessCore 1.66.0
• pRoloc 1.44.1
• pRolocdata 1.42.0
• pRolocGUI 2.14.0
• ProtGenerics 1.36.0
• PRROC 1.3.1
• PSCBS 0.67.0
• PSMatch 1.8.0
• PureCN 2.10.0
• pwalign 1.0.0
• qap-0.1-2
• QDNAseq 1.40.0
• QFeatures 1.14.1
• qlcMatrix 0.9.8
• qqconf 1.3.2
• quantsmooth 1.70.0
• qvalue 2.36.0
• R.devices 2.17.2
• R.filesets 2.15.1
• R.huge 0.10.1
• rainbow 3.8
• randomcoloR 1.1.0.1
• RBGL 1.80.0
• RcisTarget 1.24.0
• RcppAnnoy 0.0.22
• RcppHNSW 0.6.0
• RcppML 0.3.7
• RcppZiggurat 0.1.6
• reactome.db 1.88.0
• ReactomePA 1.48.0
• regioneR 1.36.0
• reldist-1.7-2
• remaCor 0.0.18
• Repitools 1.50.0
• ReportingTools 2.44.0
• ResidualMatrix 1.14.0
• restfulr 0.0.15
• Rfast 2.1.0
• RFOC-3.4-10
• rGADEM 2.52.0
• Rgraphviz 2.48.0
• rhdf5 2.48.0
• rhdf5filters 1.16.0
• Rhdf5lib 1.26.0
• Rhtslib 3.0.0
• Ringo 1.66.0
• RNASeqPower 1.44.0
• RnBeads 2.22.0
• RnBeads.hg19 1.36.0
• RnBeads.hg38 1.36.0
• RnBeads.mm10 2.12.0
• RnBeads.mm9 1.36.0
• RnBeads.rn5 1.36.0
• ROC 1.80.0
• rols 3.0.0
• ROntoTools 2.32.0
• ropls 1.36.0
• RPMG-2.2-7
• RProtoBufLib 2.16.0
• Rsamtools 2.20.0
• RSEIS-4.2-0
• Rsubread 2.18.0
• rsvd 1.0.5
• rtracklayer 1.64.0
• Rwave-2.6-5
• S4Arrays 1.4.1
• S4Vectors 0.42.0
• samr 3.0
• SamSPECTRAL 1.58.0
• SC3 1.32.0
• ScaledMatrix 1.12.0
• SCANVIS 1.18.0
• scater 1.32.0
• scattermore 1.2
• scDblFinder 1.18.0
• scistreer 1.2.0
• scran 1.32.0
• scrime 1.3.5
• scuttle 1.14.0
• SeqArray 1.44.0
• seqLogo 1.70.0
• SeqVarTools 1.42.0
• seriation 1.5.5
• Seurat 5.1.0
• SeuratObject 5.0.2
• shinyBS 0.61.1
• shinydashboardPlus 2.0.4
• shinyFiles 0.9.3
• shinyhelper 0.3.2
• shinypanel 0.1.5
• shinyWidgets 0.8.6
• ShortRead 1.62.0
• siggenes 1.78.0
• Signac 1.13.0
• simplifyEnrichment 1.14.0
• SingleCellExperiment 1.26.0
• SingleR 2.6.0
• sitmo 2.0.2
• slingshot 2.12.0
• SMVar 1.3.4
• SNPRelate 1.38.0
• snpStats 1.54.0
• SparseArray 1.4.8
• sparseMatrixStats 1.16.0
• sparsesvd-0.2-2
• SpatialExperiment 1.14.0
• Spectra 1.14.1
• SPIA 2.56.0
• splancs-2.01-45
• SPOTlight 1.8.0
• stageR 1.26.0
• struct 1.16.0
• structToolbox 1.16.0
• SummarizedExperiment 1.34.0
• susieR 0.12.35
• sva 3.52.0
• TailRank 3.2.2
• TFBSTools 1.42.0
• TFMPvalue 0.0.9
• tkWidgets 1.82.0
• TrajectoryUtils 1.12.0
• treeio 1.28.0
• TreeSummarizedExperiment 2.12.0
• TSP-1.2-4
• TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
• TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
• txdbmaker 1.0.0
• tximport 1.32.0
• UCell 2.8.0
• UCSC.utils 1.0.0
• universalmotif 1.22.0
• uwot 0.2.2
• variancePartition 1.34.0
• VariantAnnotation 1.50.0
• venn 1.12
• vsn 3.72.0
• waiter 0.2.5
• wateRmelon 2.10.0
• WGCNA-1.72-5
• widgetTools 1.82.0
• Wrench 1.22.0
• xcms 4.2.2
• XVector 0.44.0
• zCompositions-1.5.0-4
• zellkonverter 1.14.0
• zlibbioc 1.50.0

More Information

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

Dependencies

This version of R-bundle-Bioconductor has a direct dependency on: arrow-R/14.0.1-foss-2023a-R-4.4.1 Boost/1.82.0-GCC-12.3.0 foss/2023a GSL/2.7-GCC-12.3.0 R/4.4.1-gfbf-2023a

Required By

This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2023a-foss-2023a-R-4.4.1

Other Versions

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

Last modified on 28th June 2024