BiocParallel

DOI: 10.18129/B9.bioc.BiocParallel  

Bioconductor facilities for parallel evaluation

Bioconductor version: Release (3.17)

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>

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")

 

PDF	R Script	2. Introduction to BatchtoolsParam
PDF	R Script	3. Errors, Logs and Debugging
HTML	R Script	4. Random Numbers in BiocParallel
HTML	R Script	Introduction to BiocParallel
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software
Version	1.34.2
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	GPL-2 | GPL-3
Depends	methods, R (>= 3.5.0)
Imports	stats, utils, futile.logger, parallel, snow, codetools
LinkingTo	BH, cpp11
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
SystemRequirements	C++11
Enhances	Rmpi
URL	https://github.com/Bioconductor/BiocParallel
BugReports	https://github.com/Bioconductor/BiocParallel/issues
Depends On Me	bacon, BEclear, Cardinal, ChIPQC, ClassifyR, clusterSeq, consensusSeekeR, CopywriteR, 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, ASpediaFI, 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, cellbaseR, CellBench, CelliD, CellMixS, censcyt, Cepo, ChIPexoQual, ChromSCape, chromswitch, chromVAR, CNVMetrics, CNVRanger, CoGAPS, comapr, coMethDMR, CompoundDb, concordexR, condiments, consensusDE, consICA, contiBAIT, CoreGx, coseq, cpvSNP, CrispRVariants, csaw, CTSV, cydar, CytoGLMM, cytoKernel, cytomapper, CytoPipeline, dasper, dcGSA, debCAM, DepInfeR, derfinder, DEScan2, DESeq2, DEsingle, DESpace, DiffBind, Dino, dmrseq, DOSE, DRIMSeq, DropletUtils, Dune, easier, easyRNASeq, EMDomics, enhancerHomologSearch, epimutacions, epistasisGA, erma, ERSSA, escape, EWCE, exomePeak2, ExpHunterSuite, factR, fgsea, FindIT2, flowcatchR, flowSpecs, GDCRNATools, GENESIS, GenomAutomorphism, GenomicAlignments, genotypeeval, 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, MethCP, MethylAid, methylGSA, methylInheritance, methylscaper, MetNet, mia, miaViz, microbiomeMarker, microSTASIS, MIGSA, miloR, minfi, mixOmics, MMAPPR2, MOGAMUN, MoleculeExperiment, monaLisa, motifbreakR, MPRAnalyze, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MSnbase, msqrob2, MsQuality, MSstatsSampleSize, multiHiCcompare, mumosa, muscat, NBAMSeq, NBSplice, nnSVG, NPARC, NxtIRFcore, OmicsLonDA, ORFik, OVESEG, PAIRADISE, pairedGSEA, PCAtools, PDATK, pengls, PharmacoGx, pipeComp, pram, PrecisionTrialDrawer, proActiv, proFIA, profileplyr, ProteoDisco, PSMatch, qpgraph, qsea, QuasR, RadioGx, Rcwl, recount, RegEnrich, REMP, RiboCrypt, RJMCMCNucleosomes, RNAmodR, Rsamtools, RUVcorr, satuRn, scanMiR, scanMiRApp, SCArray, SCArray.sat, scater, scClassify, scDblFinder, scDD, scDDboost, scde, 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, TarSeqQC, 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, glmGamPoi, GRaNIE, HDF5Array, ISAnalytics, MethylAidData, MungeSumstats, netSmooth, omicsPrint, pareg, 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

Package Archives

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

Source Package	BiocParallel_1.34.2.tar.gz
Windows Binary	BiocParallel_1.34.2.zip (64-bit only)
macOS Binary (x86_64)	BiocParallel_1.34.2.tgz
macOS Binary (arm64)	BiocParallel_1.34.2.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 3.17	Source Archive