BiocParallel

DOI: 10.18129/B9.bioc.BiocParallel    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BiocParallel.

Bioconductor facilities for parallel evaluation

Bioconductor version: 3.12

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Author: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Valerie Obenchain [aut], Michel Lang [aut], Ryan Thompson [aut], Nitesh Turaga [aut], Aaron Lun [ctb]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocParallel")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiocParallel")

 

PDF	R Script	1. Introduction to BiocParallel
PDF	R Script	2. Introduction to BatchtoolsParam
PDF	R Script	3. Errors, Logs and Debugging
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software
Version	1.24.1
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	GPL-2 | GPL-3
Depends	methods
Imports	stats, utils, futile.logger, parallel, snow
LinkingTo	BH
Suggests	BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table
SystemRequirements	C++11
Enhances
URL	https://github.com/Bioconductor/BiocParallel
BugReports	https://github.com/Bioconductor/BiocParallel/issues
Depends On Me	bacon, BEclear, Cardinal, ClassifyR, clusterSeq, consensusSeekeR, CopywriteR, deco, DEWSeq, DEXSeq, DMCFB, DMCHMM, doppelgangR, DSS, FRASER, GenomicFiles, hiReadsProcessor, INSPEcT, matter, MBASED, metagene, metagene2, ncGTW, Oscope, OUTRIDER, PCAN, periodicDNA, pRoloc, Rqc, sequencing, ShortRead, SigCheck, Spectra, STROMA4, SummarizedBenchmark, sva, variancePartition, xcms
Imports Me	abseqR, ADImpute, AffiXcan, ALDEx2, AlphaBeta, ALPS, AlpsNMR, amplican, ASICS, ASpediaFI, atSNP, bambu, BANDITS, BASiCS, batchelor, bayNorm, BiocNeighbors, BioCor, BiocSingular, BioMM, BioNetStat, biotmle, biscuiteer, bluster, brendaDb, bsseq, CAGEfightR, CAGEr, cellbaseR, CellBench, CellMixS, ChIPexoQual, ChIPQC, ChromSCape, chromswitch, chromVAR, CNVRanger, CoGAPS, consensusDE, contiBAIT, CoreGx, coseq, cpvSNP, CRISPRseek, CrispRVariants, csaw, cydar, dasper, dcGSA, debCAM, DEComplexDisease, DelayedMatrixStats, derfinder, DEScan2, DESeq2, DEsingle, DiffBind, dmrseq, DOSE, DRIMSeq, DropletUtils, Dune, easyRNASeq, EMDomics, erma, ERSSA, escape, exomePeak2, fgsea, FindMyFriends, flowcatchR, flowSpecs, GDCRNATools, GenoGAM, GenomicAlignments, genotypeeval, gmapR, gscreend, GSEABenchmarkeR, GSVA, GUIDEseq, h5vc, HiCBricks, HiCcompare, HTSeqGenie, HTSFilter, iasva, icetea, ideal, IHWpaper, IMAS, ImpulseDE2, InPAS, IntEREst, IONiseR, IPO, ISAnalytics, IVAS, JunctionSeq, KinSwingR, LineagePulse, loci2path, LowMACA, MACPET, mbkmeans, MCbiclust, metabomxtr, metaseqR2, MethCP, MethylAid, methylGSA, methylInheritance, methyvim, MetNet, MIGSA, minfi, mixOmics, MMAPPR2, MOGAMUN, motifbreakR, MPRAnalyze, MSnbase, MSstatsSampleSize, multiHiCcompare, muscat, NBAMSeq, NBSplice, NPARC, OmicsLonDA, ORFik, OVESEG, PAIRADISE, PCAtools, PharmacoGx, pipeComp, pram, PrecisionTrialDrawer, proActiv, proFIA, profileplyr, qpgraph, qsea, QuasR, RadioGx, Rcwl, recount, RegEnrich, REMP, RJMCMCNucleosomes, RNAmodR, Rsamtools, RUVcorr, scater, scClassify, scDblFinder, scDD, scde, SCFA, scHOT, scMerge, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, scruff, scTHI, scuttle, sesame, SEtools, sigFeature, signatureSearch, singleCellTK, SingleR, singscore, SNPhood, soGGi, SpectralTAD, spicyR, splatter, SplicingGraphs, srnadiff, TAPseq, TarSeqQC, TBSignatureProfiler, TFBSTools, TMixClust, ToxicoGx, TPP2D, tradeSeq, trena, Trendy, TSRchitect, TVTB, TxRegInfra, VariantFiltering, VariantTools, velociraptor, waddR, weitrix, zinbwave
Suggests Me	beachmat, CAGEWorkflow, chimera, curatedMetagenomicData, DelayedArray, glmGamPoi, HDF5Array, MethylAidData, netSmooth, omicsPrint, PureCN, randRotation, RcisTarget, scGPS, SeqArray, systemPipeR, TENxBrainData, TENxPBMCData, TFutils, TileDBArray, tofsims, TSCAN, universalmotif
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BiocParallel_1.24.1.tar.gz
Windows Binary	BiocParallel_1.24.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	BiocParallel_1.24.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocParallel
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocParallel
Package Short Url	https://bioconductor.org/packages/BiocParallel/
Package Downloads Report	Download Stats