BiocParallel

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see BiocParallel.

Bioconductor facilities for parallel evaluation

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

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

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/

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