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BiocParallel

Bioconductor facilities for parallel evaluation


Bioconductor version: Release (3.18)

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

Author: Martin Morgan [aut, cre], Jiefei Wang [aut], Valerie Obenchain [aut], Michel Lang [aut], Ryan Thompson [aut], Nitesh Turaga [aut], Aaron Lun [ctb], Henrik Bengtsson [ctb], Madelyn Carlson [ctb] (Translated 'Random Numbers' vignette from Sweave to RMarkdown / HTML.), Phylis Atieno [ctb] (Translated 'Introduction to BiocParallel' vignette from Sweave to Rmarkdown / HTML.), Sergio Oller [ctb] (Improved bpmapply() efficiency., )

Maintainer: Martin Morgan <mtmorgan.bioc at gmail.com>

Citation (from within R, enter citation("BiocParallel")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
1. Introduction to BiocParallel HTML R Script
2. Introduction to BatchtoolsParam PDF R Script
3. Errors, Logs and Debugging PDF R Script
4. Random Numbers in BiocParallel HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software
Version 1.36.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2 | GPL-3
Depends methods, R (>= 3.5.0)
Imports stats, utils, futile.logger, parallel, snow, codetools
System Requirements C++11
URL https://github.com/Bioconductor/BiocParallel
Bug Reports https://github.com/Bioconductor/BiocParallel/issues
See More
Suggests BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table
Linking To BH, cpp11
Enhances Rmpi
Depends On Me bacon, BEclear, Cardinal, ChIPQC, ClassifyR, clusterSeq, consensusSeekeR, deco, DEWSeq, DEXSeq, DMCFB, DMCHMM, doppelgangR, DSS, extraChIPs, FEAST, FRASER, GenomicFiles, hiReadsProcessor, INSPEcT, iPath, ISLET, matter, MBASED, metagene, metagene2, metapone, ncGTW, Oscope, OUTRIDER, PCAN, periodicDNA, pRoloc, RedisParam, Rqc, sequencing, ShortRead, SigCheck, Spectra, STROMA4, SummarizedBenchmark, sva, variancePartition, xcms
Imports Me abseqR, ADImpute, AffiXcan, ALDEx2, AlphaBeta, AlpsNMR, amplican, ASICS, atena, atSNP, bambu, BANDITS, bandle, BASiCS, batchelor, bayNorm, beer, benchdamic, BiocNeighbors, BioCor, BiocSingular, BioMM, BioNERO, BioNetStat, biotmle, biscuiteer, bluster, brendaDb, bsseq, CAGEfightR, CAGEr, CBEA, ccImpute, CDI, cellbaseR, CellBench, CelliD, CellMixS, censcyt, Cepo, ChIPexoQual, ChromSCape, chromVAR, CNVMetrics, CNVRanger, CoGAPS, comapr, coMethDMR, CompoundDb, concordexR, condiments, consensusDE, consICA, contiBAIT, CoreGx, coseq, cpvSNP, CrispRVariants, csaw, CTSV, cydar, CytoGLMM, cytoKernel, cytomapper, CytoPipeline, dcGSA, debCAM, DepInfeR, derfinder, DEScan2, DESeq2, DEsingle, DESpace, DiffBind, Dino, dmrseq, DOSE, doubletrouble, dreamlet, DRIMSeq, DropletUtils, Dune, easier, easyRNASeq, EMDomics, enhancerHomologSearch, epimutacions, epistasisGA, erma, ERSSA, escape, EWCE, exomePeak2, ExpHunterSuite, factR, fgsea, FindIT2, flowcatchR, flowSpecs, GDCRNATools, gDNAx, gDRcore, gDRutils, GENESIS, GenomAutomorphism, GenomicAlignments, GloScope, gmapR, gscreend, GSEABenchmarkeR, GSVA, h5vc, HiCBricks, HiCcompare, HiCDOC, HiCExperiment, HiContacts, HTSeqGenie, HTSFilter, iasva, icetea, ideal, IHWpaper, IMAS, imcRtools, IntEREst, IONiseR, IPO, IsoformSwitchAnalyzeR, IVAS, katdetectr, KinSwingR, LineagePulse, lisaClust, loci2path, LowMACA, LRcell, Macarron, magpie, magrene, mariner, mbkmeans, MCbiclust, MetaboAnnotation, metabomxtr, metaseqR2, MethylAid, methylGSA, methylInheritance, methylscaper, MetNet, mia, miaViz, microbiomeMarker, microSTASIS, MICSQTL, miloR, minfi, mixOmics, MMAPPR2, MOGAMUN, MoleculeExperiment, monaLisa, motifbreakR, MPRAnalyze, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MSnbase, msqrob2, MsQuality, MSstatsSampleSize, multiHiCcompare, mumosa, muscat, NBAMSeq, nnSVG, NPARC, OmicsLonDA, ORFik, orthos, OVESEG, PAIRADISE, pairedGSEA, PCAtools, PDATK, pengls, PharmacoGx, pipeComp, pram, proActiv, profileplyr, ProteoDisco, PSMatch, qpgraph, qsea, QuasR, RadioGx, raer, Rcwl, recount, RegEnrich, REMP, RiboCrypt, RJMCMCNucleosomes, RNAmodR, RNAseqCovarImpute, Rsamtools, RUVcorr, satuRn, scanMiR, scanMiRApp, SCArray, SCArray.sat, scater, scClassify, scDblFinder, scDD, scDDboost, scde, scDesign3, SCFA, scFeatures, scHOT, scMerge, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, screenCounter, scruff, scShapes, scTHI, scuttle, seqArchR, seqArchRplus, seqpac, sesame, SEtools, sigFeature, signatureSearch, SimBu, simpleSeg, singleCellTK, SingleR, singscore, SNPhood, soGGi, sparrow, SpatialFeatureExperiment, SpectralTAD, spicyR, splatter, SpliceWiz, SplicingGraphs, srnadiff, Statial, STdeconvolve, SUITOR, syntenet, TAPseq, TBSignatureProfiler, ternarynet, TFBSTools, TMixClust, ToxicoGx, TPP2D, tradeSeq, TreeSummarizedExperiment, Trendy, TVTB, txcutr, UCell, VariantFiltering, VariantTools, VDJdive, velociraptor, Voyager, waddR, weitrix, zinbwave
Suggests Me alabaster.mae, beachmat, CAGEWorkflow, DelayedArray, DIAlignR, EpiCompare, GenomicDataCommons, ggsc, glmGamPoi, GRaNIE, HDF5Array, ISAnalytics, MethylAidData, MungeSumstats, netSmooth, omicsPrint, pareg, plyinteractions, PureCN, randRotation, RcisTarget, rebook, rhdf5, S4Arrays, scGPS, SeqArray, Single.mTEC.Transcriptomes, spatialHeatmap, TENxBrainData, TENxPBMCData, TFutils, TileDBArray, TrajectoryUtils, trena, TSCAN, universalmotif, xcore
Links To Me
Build Report Build Report

Package Archives

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

Source Package BiocParallel_1.36.0.tar.gz
Windows Binary BiocParallel_1.36.0.zip
macOS Binary (x86_64) BiocParallel_1.36.0.tgz
macOS Binary (arm64) BiocParallel_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocParallel
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocParallel
Bioc Package Browser https://code.bioconductor.org/browse/BiocParallel/
Package Short Url https://bioconductor.org/packages/BiocParallel/
Package Downloads Report Download Stats