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
Architectures
EL8-cascadelake — EL8-icelake — EL8-sapphirerapids
The listed architectures consist of two parts: 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 DMRcaller/1.36.0-foss-2023a-R-4.4.1 inferCNV/1.20.0-foss-2023a-R-4.4.1 methylKit/1.30.0-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