R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0
There is a newer version of R-bundle-Bioconductor
R is a free software environment for statistical computing and graphics.Accessing R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0
To load the module for R-bundle-Bioconductor 3.13-foss-2021a-R-4.1.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load R-bundle-Bioconductor/3.13-foss-2021a-R-4.1.0
BEAR Apps Version
Extensions
- admisc 0.15
- affxparser 1.64.0
- affy 1.70.0
- affycoretools 1.64.0
- affyio 1.62.0
- AgiMicroRna 2.42.0
- agricolae-1.3-3
- ALDEx2 1.24.0
- ALL 1.34.0
- annaffy 1.63.1
- annotate 1.70.0
- AnnotationDbi 1.54.0
- AnnotationFilter 1.16.0
- AnnotationForge 1.34.0
- AnnotationHub 3.0.0
- aroma.affymetrix 3.2.0
- aroma.apd 0.6.0
- aroma.core 3.2.2
- aroma.light 3.22.0
- ash-1.0-15
- ATACseqQC 1.16.0
- aws.s3 0.3.21
- aws.signature 0.6.0
- ballgown 2.24.0
- batchelor 1.8.0
- baySeq 2.26.0
- beachmat 2.8.0
- Biobase 2.52.0
- BiocFileCache 2.0.0
- BiocGenerics 0.38.0
- BiocIO 1.2.0
- BiocManager 1.30.15
- BiocNeighbors 1.10.0
- BiocParallel 1.26.0
- BiocSingular 1.8.0
- BiocStyle 2.20.0
- BiocVersion 3.13.1
- biomaRt 2.48.0
- biomformat 1.20.0
- Biostrings 2.60.0
- biovizBase 1.40.0
- blme-1.0-5
- bluster 1.2.1
- bookdown 0.22
- BSgenome 1.60.0
- BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0
- BSgenome.Hsapiens.UCSC.hg19 1.4.3
- BSgenome.Hsapiens.UCSC.hg38 1.4.3
- BSgenome.Mmusculus.UCSC.mm10 1.4.0
- bumphunter 1.34.0
- CAMERA 1.48.0
- Category 2.58.0
- ccdata 1.18.0
- ccmap 1.18.0
- CGHbase 1.52.0
- ChIPpeakAnno 3.26.0
- CNEr 1.28.0
- coloc-3.2-1
- colorRamps 2.3
- ComplexHeatmap 2.8.0
- ConsensusClusterPlus 1.56.0
- conumee 1.26.0
- crossmeta 1.18.0
- cummeRbund 2.34.0
- cytolib 2.4.0
- CytoML 2.4.0
- dada2 1.20.0
- DeconRNASeq 1.34.0
- DEGseq 1.46.0
- DelayedArray 0.18.0
- DelayedMatrixStats 1.14.0
- derfinder 1.26.0
- derfinderHelper 1.26.0
- DESeq2 1.32.0
- diffcyt 1.12.0
- DirichletMultinomial 1.34.0
- DNAcopy 1.66.0
- docopt 0.7.1
- dqrng 0.3.0
- DRIMSeq 1.20.0
- DropletUtils 1.12.1
- dupRadar 1.22.0
- DynDoc 1.70.0
- EBImage 4.34.0
- edgeR 3.34.0
- egg 0.4.5
- emmeans 1.6.1
- EnsDb.Hsapiens.v75 2.99.0
- EnsDb.Hsapiens.v86 2.99.0
- ensembldb 2.16.0
- estimability 1.3
- ExperimentHub 2.0.0
- extraDistr 1.9.1
- fda 5.1.9
- FDb.InfiniumMethylation.hg19 2.2.0
- fds 1.8
- fgsea 1.18.0
- filelock 1.0.2
- flowClust 3.30.0
- flowCore 2.4.0
- FlowSOM 2.0.0
- FlowSorted.Blood.EPIC 1.10.1
- FlowSorted.CordBloodCombined.450k 1.8.0
- flowStats 4.4.0
- flowViz 1.56.0
- flowWorkspace 4.4.0
- FRASER 1.4.0
- fresh 0.2.0
- gcrma 2.64.0
- gdsfmt 1.28.0
- GenABEL-1.8-0
- GenABEL.data 1.0.0
- genefilter 1.74.0
- geneLenDataBase 1.28.0
- geneplotter 1.70.0
- GENESIS 2.22.0
- GENIE3 1.14.0
- GenomeInfoDb 1.28.0
- GenomeInfoDbData 1.2.6
- GenomicAlignments 1.28.0
- GenomicFeatures 1.44.0
- GenomicFiles 1.28.0
- GenomicRanges 1.44.0
- GenomicScores 2.4.0
- GEOquery 2.60.0
- ggbio 1.40.0
- ggcyto 1.20.0
- ggdendro 0.1.22
- ggnewscale 0.4.5
- ggpointdensity 0.1.0
- ggseqlogo 0.1
- ggthemes 4.2.4
- GLAD 2.56.0
- Glimma 2.2.0
- GlobalAncova 4.10.0
- globaltest 5.46.0
- GO.db 3.13.0
- goseq 1.44.0
- GOstats 2.58.0
- graph 1.70.0
- GSEABase 1.54.0
- gsmoothr 0.1.7
- GSVA 1.40.0
- Gviz 1.36.1
- GWASExactHW 1.01
- GWASTools 1.38.0
- HDF5Array 1.20.0
- hdrcde 3.4
- heatmaply 1.2.1
- hgu133plus2.db 3.13.0
- HMMcopy 1.34.0
- Homo.sapiens 1.3.1
- IHW 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 0.34.0
- impute 1.66.0
- InteractionSet 1.20.0
- interactiveDisplayBase 1.30.0
- IRanges 2.26.0
- isva 1.9
- JASPAR2020 0.99.10
- KEGG.db 3.2.4
- KEGGgraph 1.52.0
- KEGGREST 1.32.0
- LEA 3.4.0
- limma 3.48.0
- lpsymphony 1.20.0
- lsa 0.73.2
- lumi 2.44.0
- marray 1.70.0
- maSigPro 1.64.0
- MassSpecWavelet 1.58.0
- mathjaxr-1.4-0
- MatrixGenerics 1.4.0
- MEDIPS 1.44.0
- metagenomeSeq 1.34.0
- metaMA 3.1.2
- metap 1.4
- metapod 1.0.0
- MethylSeekR 1.32.0
- methylumi 2.38.0
- Mfuzz 2.52.0
- minfi 1.38.0
- missMethyl 1.26.0
- mixOmics 6.16.0
- MLInterfaces 1.72.0
- MotifDb 1.34.0
- motifmatchr 1.14.0
- motifStack 1.36.0
- MsCoreUtils 1.4.0
- MSnbase 2.18.0
- MultiDataSet 1.20.0
- multtest 2.48.0
- muscat 1.6.0
- mutoss-0.1-12
- mzID 1.30.0
- mzR 2.26.0
- NADA-1.6-1.1
- ncdfFlow 2.38.0
- NOISeq 2.36.0
- oligo 1.56.0
- oligoClasses 1.54.0
- ontologyIndex 2.7
- openCyto 2.4.0
- org.Hs.eg.db 3.13.0
- org.Mm.eg.db 3.13.0
- org.Rn.eg.db 3.13.0
- OrganismDbi 1.34.0
- OUTRIDER 1.10.0
- pcaMethods 1.84.0
- perm-1.0-0.0
- PFAM.db 3.13.0
- phyloseq 1.36.0
- pmp 1.4.0
- polyester 1.28.0
- poweRlaw 0.70.6
- preprocessCore 1.54.0
- pRoloc 1.32.0
- pRolocdata 1.30.0
- pRolocGUI 2.2.0
- ProtGenerics 1.24.0
- PRROC 1.3.1
- PSCBS 0.65.0
- PureCN 1.22.1
- qap-0.1-1
- qlcMatrix 0.9.7
- quantsmooth 1.58.0
- qvalue 2.24.0
- 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 1.68.0
- RcppAnnoy 0.0.18
- RcppHNSW 0.3.0
- RcppZiggurat 0.1.6
- regioneR 1.24.0
- Repitools 1.38.0
- ReportingTools 2.32.0
- ResidualMatrix 1.2.0
- restfulr 0.0.13
- Rfast 2.0.3
- rGADEM 2.40.0
- Rgraphviz 2.36.0
- rhdf5 2.36.0
- rhdf5filters 1.4.0
- Rhdf5lib 1.14.0
- Rhtslib 1.24.0
- Ringo 1.56.0
- RNASeqPower 1.32.0
- ROC 1.68.0
- ropls 1.24.0
- RProtoBufLib 2.4.0
- Rsamtools 2.8.0
- Rsolnp 1.16
- RSpectra-0.16-0
- Rsubread 2.6.1
- rsvd 1.0.5
- rtracklayer 1.52.0
- S4Vectors 0.30.0
- samr 3.0
- SC3 1.20.0
- ScaledMatrix 1.0.0
- SCANVIS 1.6.0
- scater 1.20.0
- scattermore 0.7
- scran 1.20.1
- scrime 1.3.5
- sctransform 0.3.2
- scuttle 1.2.0
- SeqArray 1.32.0
- seqLogo 1.58.0
- SeqVarTools 1.30.0
- seriation-1.2-9
- Seurat 4.0.3
- SeuratObject 4.0.2
- shinyBS 0.61
- shinydashboardPlus 2.0.1
- shinyFiles 0.9.0
- shinyhelper 0.3.2
- shinypanel 0.1.4
- shinyWidgets 0.6.0
- ShortRead 1.50.0
- siggenes 1.66.0
- Signac 1.2.1
- SingleCellExperiment 1.14.1
- SingleR 1.6.1
- sitmo 2.0.1
- SMVar 1.3.3
- SNPRelate 1.26.0
- snpStats 1.42.0
- sparseMatrixStats 1.4.0
- sparsesvd 0.2
- SPIA 2.44.0
- stageR 1.14.0
- struct 1.4.0
- structToolbox 1.4.0
- SummarizedExperiment 1.22.0
- sva 3.40.0
- TFBSTools 1.30.0
- TFMPvalue 0.0.8
- tkWidgets 1.70.0
- truncnorm-1.0-8
- TSP-1.1-10
- TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
- TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0
- tximport 1.20.0
- uwot 0.1.10
- variancePartition 1.22.0
- VariantAnnotation 1.38.0
- venn 1.10
- vsn 3.60.0
- waiter 0.2.1
- wateRmelon 1.36.0
- widgetTools 1.70.0
- Wrench 1.10.0
- xcms 3.14.0
- XVector 0.32.0
- zCompositions 1.3.4
- zlibbioc 1.38.0
More Information
For more information visit the R-bundle-Bioconductor website.
Dependencies
This version of R-bundle-Bioconductor has a direct dependency on: Boost/1.76.0-GCC-10.3.0 foss/2021a GSL/2.7-GCC-10.3.0 HDF5/1.10.7-gompi-2021a ncdf4/1.17-foss-2021a-R-4.1.0 R/4.1.0-foss-2021a
Required By
This version of R-bundle-Bioconductor is a direct dependent of: BEAR-R-bio/2021a-foss-2021a-R-4.1.0 CAGEr/1.34.0-foss-2021a-R-4.1.0 ChIPseeker/1.28.3-foss-2021a-R-4.1.0 GeomxTools/1.0.0-foss-2021a-R-4.1.0 gsfisher/3ad1d79-foss-2021a-R-4.1.0 iClusterPlus/1.28.0-foss-2021a PharmacoGx/2.4.0-foss-2021a phenoptrReports/0.3.0-foss-2021a-R-4.1.0 rcdk/3.6.0-foss-2021a survcomp/1.42.0-foss-2021a
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 13th September 2021