R-bundle-Bioconductor 3.15-foss-2021b-R-4.2.0
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R is a free software environment for statistical computing and graphics.Accessing R-bundle-Bioconductor 3.15-foss-2021b-R-4.2.0
To load the module for R-bundle-Bioconductor 3.15-foss-2021b-R-4.2.0 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/3.15-foss-2021b-R-4.2.0
BEAR Apps Version
Extensions
- admisc 0.27
- affxparser 1.68.1
- affy 1.74.0
- affycoretools 1.68.0
- affyio 1.66.0
- AgiMicroRna 2.46.0
- agricolae-1.3-5
- ALDEx2 1.28.0
- ALL 1.38.0
- annaffy 1.68.0
- annotate 1.74.0
- AnnotationDbi 1.58.0
- AnnotationFilter 1.20.0
- AnnotationForge 1.38.0
- AnnotationHub 3.4.0
- aroma.affymetrix 3.2.0
- aroma.apd 0.6.0
- aroma.core 3.2.2
- aroma.light 3.26.0
- ash-1.0-15
- ATACseqQC 1.20.2
- AUCell 1.18.0
- aws.s3 0.3.21
- aws.signature 0.6.0
- ballgown 2.28.0
- batchelor 1.12.0
- baySeq 2.30.0
- beachmat 2.12.0
- Biobase 2.56.0
- BiocFileCache 2.4.0
- BiocGenerics 0.42.0
- BiocIO 1.6.0
- BiocManager 1.30.17
- BiocNeighbors 1.14.0
- BiocParallel 1.30.0
- BiocSingular 1.12.0
- BiocStyle 2.24.0
- BiocVersion 3.15.2
- biomaRt 2.52.0
- biomformat 1.24.0
- Biostrings 2.64.0
- biovizBase 1.44.0
- blme-1.0-5
- bluster 1.6.0
- bookdown 0.26
- BSgenome 1.64.0
- BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0
- BSgenome.Hsapiens.UCSC.hg19 1.4.3
- BSgenome.Hsapiens.UCSC.hg38 1.4.4
- BSgenome.Mmusculus.UCSC.mm10 1.4.3
- bsseq 1.32.0
- bumphunter 1.38.0
- CAGEr 2.2.0
- CAMERA 1.52.0
- Category 2.62.0
- ccdata 1.22.0
- ccmap 1.22.0
- CGHbase 1.56.0
- ChIPpeakAnno 3.30.0
- chromVAR 1.18.0
- CNEr 1.32.0
- coloc 5.1.0
- colorRamps 2.3.1
- ComplexHeatmap 2.12.0
- ConsensusClusterPlus 1.60.0
- conumee 1.30.0
- crossmeta 1.22.0
- cummeRbund 2.38.0
- cytolib 2.8.0
- CytoML 2.8.0
- dada2 1.24.0
- DeconRNASeq 1.38.0
- DEGseq 1.50.0
- DelayedArray 0.22.0
- DelayedMatrixStats 1.18.0
- densEstBayes-1.0-2.1
- derfinder 1.30.0
- derfinderHelper 1.30.0
- DESeq2 1.36.0
- diffcyt 1.16.0
- DirichletMultinomial 1.38.0
- DNABarcodes 1.26.0
- DNAcopy 1.70.0
- docopt 0.7.1
- dqrng 0.3.0
- DRIMSeq 1.24.0
- DropletUtils 1.16.0
- DSS 2.44.0
- dupRadar 1.26.0
- DynDoc 1.74.0
- EBImage 4.38.0
- edgeR 3.38.0
- egg 0.4.5
- emmeans 1.7.3
- EnsDb.Hsapiens.v75 2.99.0
- EnsDb.Hsapiens.v79 2.99.0
- EnsDb.Hsapiens.v86 2.99.0
- ensembldb 2.20.1
- estimability 1.3
- ExomeDepth 1.1.15
- ExperimentHub 2.4.0
- extraDistr 1.9.1
- fda 6.0.3
- FDb.InfiniumMethylation.hg19 2.2.0
- fds 1.8
- fgsea 1.22.0
- filelock 1.0.2
- flowClust 3.34.0
- flowCore 2.8.0
- FlowSOM 2.4.0
- FlowSorted.Blood.EPIC 2.0.0
- FlowSorted.CordBloodCombined.450k 1.12.0
- flowStats 4.8.0
- flowViz 1.60.0
- flowWorkspace 4.8.0
- FRASER 1.8.0
- fresh 0.2.0
- gcrma 2.68.0
- gdsfmt 1.32.0
- genefilter 1.78.0
- geneLenDataBase 1.32.0
- geneplotter 1.74.0
- GENESIS 2.26.0
- GENIE3 1.18.0
- GenomeInfoDb 1.32.1
- GenomeInfoDbData 1.2.8
- GenomicAlignments 1.32.0
- GenomicFeatures 1.48.0
- GenomicFiles 1.32.0
- GenomicRanges 1.48.0
- GenomicScores 2.8.0
- GEOquery 2.64.0
- ggbio 1.44.0
- ggcyto 1.24.0
- ggdendro 0.1.23
- ggnewscale 0.4.7
- ggpointdensity 0.1.0
- ggseqlogo 0.1
- ggthemes 4.2.4
- GLAD 2.60.0
- Glimma 2.6.0
- GlobalAncova 4.14.0
- globaltest 5.50.0
- GO.db 3.15.0
- goseq 1.48.0
- GOstats 2.62.0
- graph 1.74.0
- GSEABase 1.58.0
- gsmoothr 0.1.7
- GSVA 1.44.0
- Gviz 1.40.0
- GWASExactHW 1.01
- GWASTools 1.42.0
- HDF5Array 1.24.0
- hdrcde 3.4
- heatmaply 1.3.0
- hgu133plus2.db 3.13.0
- HMMcopy 1.38.0
- Homo.sapiens 1.3.1
- IHW 1.24.0
- 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 0.38.0
- impute 1.70.0
- InteractionSet 1.24.0
- interactiveDisplayBase 1.34.0
- IRanges 2.30.0
- isva 1.9
- JASPAR2020 0.99.10
- KEGGgraph 1.56.0
- KEGGREST 1.36.0
- LEA 3.8.0
- limma 3.52.0
- lpsymphony 1.24.0
- lsa 0.73.2
- lumi 2.48.0
- M3Drop 1.22.0
- marray 1.74.0
- maSigPro 1.68.0
- MassSpecWavelet 1.62.0
- MatrixGenerics 1.8.0
- MEDIPS 1.48.0
- metagenomeSeq 1.38.0
- metaMA 3.1.3
- metap 1.8
- metapod 1.4.0
- MethylSeekR 1.36.0
- methylumi 2.42.0
- Mfuzz 2.56.0
- minfi 1.42.0
- missMethyl 1.30.0
- mixOmics 6.20.0
- mixsqp-0.3-43
- MLInterfaces 1.76.0
- MotifDb 1.38.0
- motifmatchr 1.18.0
- motifStack 1.40.0
- MsCoreUtils 1.8.0
- MsFeatures 1.4.0
- MSnbase 2.22.0
- MultiAssayExperiment 1.22.0
- MultiDataSet 1.24.0
- multtest 2.52.0
- muscat 1.10.0
- mutoss-0.1-12
- mzID 1.34.0
- mzR 2.30.0
- NADA-1.6-1.1
- ncdfFlow 2.42.0
- NMF 0.24.0
- NOISeq 2.40.0
- oligo 1.60.0
- oligoClasses 1.58.0
- ontologyIndex 2.7
- openCyto 2.8.0
- org.Hs.eg.db 3.15.0
- org.Mm.eg.db 3.15.0
- org.Rn.eg.db 3.15.0
- OrganismDbi 1.38.0
- OUTRIDER 1.14.0
- pathview 1.36.0
- pcaMethods 1.88.0
- perm-1.0-0.2
- PFAM.db 3.15.0
- phyloseq 1.40.0
- pmp 1.8.0
- polyester 1.32.0
- poweRlaw 0.70.6
- preprocessCore 1.58.0
- pRoloc 1.36.0
- pRolocdata 1.34.0
- pRolocGUI 2.6.0
- ProtGenerics 1.28.0
- PRROC 1.3.1
- PSCBS 0.66.0
- PureCN 2.2.0
- qap-0.1-1
- qlcMatrix 0.9.7
- qqconf 1.2.3
- quantsmooth 1.62.0
- qvalue 2.28.0
- 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 1.72.0
- RcisTarget 1.16.0
- RcppAnnoy 0.0.19
- RcppHNSW 0.3.0
- RcppML 0.3.7
- RcppZiggurat 0.1.6
- regioneR 1.28.0
- reldist-1.7-0
- Repitools 1.42.0
- ReportingTools 2.36.0
- ResidualMatrix 1.6.0
- restfulr 0.0.13
- Rfast 2.0.6
- rGADEM 2.44.0
- Rgraphviz 2.40.0
- rhdf5 2.40.0
- rhdf5filters 1.8.0
- Rhdf5lib 1.18.0
- RhpcBLASctl-0.21-247.1
- Rhtslib 1.28.0
- Ringo 1.60.0
- RNASeqPower 1.36.0
- ROC 1.72.0
- rols 2.24.0
- ropls 1.28.0
- RProtoBufLib 2.8.0
- Rsamtools 2.12.0
- Rsubread 2.10.0
- rsvd 1.0.5
- rtracklayer 1.56.0
- S4Vectors 0.34.0
- samr 3.0
- SC3 1.24.0
- ScaledMatrix 1.4.0
- SCANVIS 1.10.0
- scater 1.24.0
- scattermore 0.8
- scran 1.24.0
- scrime 1.3.5
- scuttle 1.6.0
- SeqArray 1.36.0
- seqLogo 1.62.0
- SeqVarTools 1.34.0
- seriation 1.3.5
- Seurat 4.1.1
- SeuratObject 4.1.0
- shinyBS 0.61.1
- shinydashboardPlus 2.0.3
- shinyFiles 0.9.1
- shinyhelper 0.3.2
- shinypanel 0.1.5
- shinyWidgets 0.6.4
- ShortRead 1.54.0
- siggenes 1.70.0
- Signac 1.6.0
- SingleCellExperiment 1.18.0
- SingleR 1.10.0
- sitmo 2.0.2
- SMVar 1.3.4
- SNPRelate 1.30.0
- snpStats 1.46.0
- sparseMatrixStats 1.8.0
- sparsesvd 0.2
- SPIA 2.48.0
- stageR 1.18.0
- struct 1.8.0
- structToolbox 1.8.0
- SummarizedExperiment 1.26.1
- susieR 0.11.92
- sva 3.44.0
- TFBSTools 1.34.0
- TFMPvalue 0.0.8
- tkWidgets 1.74.0
- TSP-1.2-0
- TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
- TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
- tximport 1.24.0
- uwot 0.1.11
- variancePartition 1.26.0
- VariantAnnotation 1.42.0
- venn 1.10
- vsn 3.64.0
- waiter 0.2.5
- wateRmelon 2.2.0
- WGCNA 1.71
- widgetTools 1.74.0
- Wrench 1.14.0
- xcms 3.18.0
- XVector 0.36.0
- zCompositions-1.4.0-1
- zlibbioc 1.42.0
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/6.0.0.2-foss-2021b-R-4.2.0 Boost/1.77.0-GCC-11.2.0 foss/2021b GSL/2.7-GCC-11.2.0 HDF5/1.12.1-gompi-2021b R/4.2.0-foss-2021b
Required By
This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2021b-foss-2021b-R-4.2.0 CellChat/1.6.0-foss-2021b-R-4.2.0 celldex/1.6.0-foss-2021b-R-4.2.0 clusterProfiler/4.4.4-foss-2021b-R-4.2.0 cyCombine/0.2.15-foss-2021b-R-4.2.0 epiAneufinder/1.0.1-foss-2021b-R-4.2.0 faahKO/1.36.0-foss-2021b-R-4.2.0 FastPG/0.0.8-foss-2021b-R-4.2.0 flowVS/1.28.0-foss-2021b-R-4.2.0 icellnet/1.0-foss-2021b-R-4.2.0 inferCNV/1.12.0-foss-2021b-R-4.2.0 maftools/2.12.0-foss-2021b-R-4.2.0 monocle/2.24.1-foss-2021b-R-4.2.0 msPurity/1.22.0-foss-2021b-R-4.2.0 MSstats/4.4.1-foss-2021b-R-4.2.0 nichenetr/20220911-foss-2021b-R-4.2.0 pandaR/1.28.0-foss-2021b-R-4.2.0 SCENIC/20220502-foss-2021b-R-4.2.0 sequenza/3.0.0-foss-2021b SpaTalk/1.0-foss-2021b-R-4.2.0
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 10th June 2022