BiocParallel

This is the released version of BiocParallel; for the devel version, see BiocParallel.

Bioconductor facilities for parallel evaluation

Bioconductor version: Release (3.23)

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

Author: Jiefei Wang [aut, cre], Martin Morgan [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., ORCID: ORCID: 0000-0002-8994-1549 )

Maintainer: Jiefei Wang <jiefei0804 at gmail.com>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") 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	HTML	R Script
3. Errors, Logs and Debugging	HTML	R Script
4. Random Numbers in BiocParallel	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software
Version	1.46.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	GPL-2 \| GPL-3 \| BSL-1.0
Depends	methods, R (>= 4.1.0)
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

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 (>= 1.87.0), cpp11
Enhances	Rmpi
Depends On Me	bacon, BEclear, Cardinal, CardinalIO, ChIPQC, Chromatograms, ClassifyR, clusterSeq, consensusSeekeR, DEWSeq, DEXSeq, DMCFB, DMCHMM, doppelgangR, DSS, extraChIPs, FEAST, FRASER, GenomicFiles, INSPEcT, iPath, ISLET, matter, MBASED, metagene2, metapone, ncGTW, Oscope, OUTRIDER, PCAN, periodicDNA, pRoloc, RedisParam, Rqc, ShortRead, SigCheck, Spectra, sva, variancePartition, xcms, sequencing, OSCA.advanced, OSCA.workflows, SingleRBook
Imports Me	abseqR, ADImpute, AffiXcan, ALDEx2, AlphaBeta, AlpsNMR, amplican, ASICS, ATACseqQC, atena, atSNP, bambu, BANDITS, bandle, Banksy, BASiCS, batchCorr, batchelor, BayesSpace, bayNorm, beer, benchdamic, BERT, betterChromVAR, BioCor, BiocSingular, BioNERO, biotmle, biscuiteer, blase, bluster, brendaDb, bsseq, CAGEfightR, CAGEr, CARDspa, carnation, CBN2Path, ccImpute, CDI, cellbaseR, CellBench, CelliD, CellMentor, CellMixS, censcyt, Cepo, ChIPexoQual, ChromSCape, chromVAR, ClusterFoldSimilarity, clustSIGNAL, CNVMetrics, CNVRanger, CoGAPS, comapr, coMethDMR, CompoundDb, concordexR, condiments, consensusOV, consICA, Coralysis, CoreGx, coseq, cpvSNP, CrispRVariants, crupR, csaw, CTSV, cydar, cypress, CytoGLMM, cytoKernel, cytomapper, CytoMDS, CytoPipeline, damidBind, dcGSA, DeconvoBuddies, decoupleR, DeepTarget, DegCre, DepInfeR, derfinder, DEScan2, DESeq2, DEsingle, DESpace, DiffBind, Dino, DMRcaller, dmrseq, DNEA, DOTSeq, dreamlet, DRIMSeq, DropletUtils, Dune, easier, easyRNASeq, EMDomics, enhancerHomologSearch, epimutacions, epiregulon, epistasisGA, ERSSA, EWCE, factR, faers, fgsea, findIPs, FindIT2, FLAMES, flowcatchR, flowSpecs, GDCRNATools, gDNAx, gDRcore, gDRutils, GeDi, GENESIS, GenomAutomorphism, GenomicAlignments, gINTomics, GloScope, gmapR, GOaGO, gscreend, GSEABenchmarkeR, GSVA, h5vc, HicAggR, HiCBricks, HiCcompare, HiCDOC, HiCExperiment, HiContacts, HTSFilter, HybridExpress, iasva, icetea, ideal, imcRtools, IntEREst, IONiseR, IPO, IsoformSwitchAnalyzeR, jazzPanda, jvecfor, katdetectr, KinSwingR, lcmsPlot, LimROTS, lisaClust, loci2path, LRcell, Macarron, magpie, magrene, mariner, mbkmeans, MCbiclust, metabinR, MetaboAnnotation, MetaboCoreUtils, metabomxtr, metaseqR2, methodical, MethylAid, methylGSA, methyLImp2, methylInheritance, methylscaper, MetNet, mia, miaViz, MICSQTL, miloR, minfi, MIRit, mist, mixOmics, MOGAMUN, MoleculeExperiment, monaLisa, MotifPeeker, MPAC, MPRAnalyze, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MSnbase, msqrob2, MsQuality, MSstatsResponse, multiHiCcompare, mumosa, muscat, NBAMSeq, nnSVG, notame, notameStats, NPARC, omicsGMF, ORFik, orthos, OVESEG, PAIRADISE, pairedGSEA, pathMED, PCAtools, PDATK, pengls, PharmacoGx, pipeComp, poem, pram, proActiv, profileplyr, ProteoDisco, PSMatch, qpgraph, QRscore, qsea, QuasR, RadioGx, raer, rawDiag, Rcwl, recount, ReducedExperiment, RegEnrich, REMP, RiboCrypt, RJMCMCNucleosomes, RNAmodR, RNAseqCovarImpute, RNAshapeQC, ROTS, Rsamtools, RUVcorr, SanityR, saseR, satuRn, scanMiR, scanMiRApp, SCArray, SCArray.sat, scater, scBubbletree, scClassify, scConform, scDblFinder, scDD, scDDboost, scde, scDesign3, SCFA, scFeatures, scGraphVerse, scHiCcompare, scHOT, scMerge, scMultiSim, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, screenCounter, scruff, scShapes, scTHI, scTypeEval, scuttle, SEraster, sesame, SEtools, sigFeature, signatureSearch, SimBu, simpleSeg, singIST, SingleCellAlleleExperiment, singleCellTK, singscore, SmartPhos, SNPhood, spacexr, SpaNorm, spARI, sparrow, SpatialFeatureExperiment, SpectralTAD, spicyR, splatter, SpliceImpactR, SpliceWiz, SplicingGraphs, spoon, SpotSweeper, srnadiff, StabMap, Statial, SUITOR, SuperCellCyto, SVP, syntenet, TAPseq, TBSignatureProfiler, ternarynet, TFBSTools, tidyCoverage, TMixClust, ToxicoGx, TPP2D, tpSVG, tradeSeq, TreeSummarizedExperiment, Trendy, TVTB, txcutr, UCell, UPDhmm, VariantFiltering, VariantTools, VDJdive, velociraptor, vmrseq, Voyager, waddR, weitrix, xCell2, zinbwave, CytoMethIC, IHWpaper, JohnsonKinaseData, ExpHunterSuite, seqpac, OSTA, causalBatch, DCLEAR, DTSEA, DysPIA, enviGCMS, GSEMA, Holomics, LDM, LOCOM2, minSNPs, oosse, robin, scGate, spatialGE
Suggests Me	alabaster.mae, beachmat, BiocNeighbors, cliqueMS, DelayedArray, EpiCompare, escape, GenomicDataCommons, ggsc, glmGamPoi, GRaNIE, h5mread, HDF5Array, imageFeatureTCGA, ISAnalytics, MeLSI, MungeSumstats, netSmooth, omicsPrint, plyinteractions, PureCN, randRotation, rebook, rhdf5, S4Arrays, scGPS, scLANE, SeqArray, SingleR, spatialHeatmap, survClust, TFutils, TileDBArray, TrajectoryUtils, TSCAN, universalmotif, xcore, MethylAidData, Single.mTEC.Transcriptomes, TENxBrainData, TENxPBMCData, CAGEWorkflow, bioLeak, clustermq, conos, easyEWAS, futurize, IOBR, pagoda2, phase1RMD, RaMS, survBootOutliers, SVG, wrTopDownFrag
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	BiocParallel_1.46.0.tar.gz
Windows Binary (x86_64)	BiocParallel_1.46.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	BiocParallel_1.46.0.tgz
macOS Binary (sonoma-arm64)	BiocParallel_1.46.0.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
Old Source Packages for BioC 3.23	Source Archive