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BiocParallel (development version)

BiocParallel

This is the development version of BiocParallel; for the stable release version, see BiocParallel.

Bioconductor facilities for parallel evaluation

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DOI: 10.18129/B9.bioc.BiocParallel

Bioconductor version: Development (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 iD ORCID: 0000-0002-8994-1549 )

Maintainer: Jiefei Wang <jiefei0804 at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 1.45.0

In Bioconductor since BioC 2.13 (R-3.0) (12 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

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 (>= 1.87.0), cpp11

Enhances Rmpi

Depends On Me bacon, BEclear, Cardinal, CardinalIO, Chromatograms, ClassifyR, clusterSeq, consensusSeekeR, DEWSeq, DEXSeq, DMCFB, DMCHMM, doppelgangR, DSS, extraChIPs, FEAST, GenomicFiles, INSPEcT, ISLET, matter, MBASED, metagene2, metapone, ncGTW, Oscope, OUTRIDER, PCAN, periodicDNA, pRoloc, RedisParam, Rqc, ShortRead, SigCheck, Spectra, sva, variancePartition, xcms, sequencing, 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, BERT, BioCor, BiocSingular, BioNERO, biotmle, biscuiteer, blase, bluster, brendaDb, bsseq, CAGEfightR, CAGEr, CARDspa, ccImpute, CDI, cellbaseR, CellBench, CelliD, CellMixS, censcyt, Cepo, ChIPexoQual, ChromSCape, ClusterFoldSimilarity, clustSIGNAL, CoGAPS, coMethDMR, CompoundDb, concordexR, condiments, consensusOV, consICA, Coralysis, CoreGx, coseq, cpvSNP, CrispRVariants, crupR, csaw, CTSV, cydar, cypress, CytoGLMM, cytoKernel, cytomapper, CytoMDS, CytoPipeline, dcGSA, decoupleR, DeepTarget, DegCre, DepInfeR, derfinder, DEScan2, DESeq2, DEsingle, DESpace, Dino, DMRcaller, dmrseq, DNEA, DOSE, dreamlet, DRIMSeq, DropletUtils, Dune, easier, easyRNASeq, EMDomics, enhancerHomologSearch, epimutacions, epiregulon, epistasisGA, ERSSA, EWCE, faers, fgsea, findIPs, FindIT2, FLAMES, flowcatchR, flowSpecs, GDCRNATools, gDNAx, gDRcore, gDRutils, GenomAutomorphism, GenomicAlignments, gscreend, GSEABenchmarkeR, GSVA, h5vc, HicAggR, HiCBricks, HiCcompare, HiCDOC, HiCExperiment, HiContacts, HTSFilter, HybridExpress, iasva, icetea, ideal, imcRtools, IONiseR, IPO, IsoformSwitchAnalyzeR, jazzPanda, katdetectr, KinSwingR, LimROTS, lisaClust, loci2path, LRcell, magpie, magrene, mariner, mbkmeans, MCbiclust, 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, NPARC, omicsGMF, ORFik, orthos, OVESEG, PAIRADISE, pairedGSEA, pathMED, PDATK, pengls, PharmacoGx, pipeComp, poem, pram, proActiv, ProteoDisco, PSMatch, qpgraph, QRscore, qsea, QuasR, RadioGx, raer, rawDiag, Rcwl, recount, ReducedExperiment, RegEnrich, REMP, RiboCrypt, RJMCMCNucleosomes, RNAmodR, RNAseqCovarImpute, ROTS, Rsamtools, RUVcorr, SanityR, saseR, satuRn, scanMiR, scanMiRApp, SCArray, scater, scBubbletree, scClassify, scDblFinder, scDD, scDDboost, scde, scDesign3, SCFA, scGraphVerse, scHiCcompare, scHOT, scMerge, scMultiSim, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, screenCounter, scruff, scShapes, scTHI, scuttle, SEraster, sesame, SEtools, sigFeature, signatureSearch, SimBu, simpleSeg, SingleCellAlleleExperiment, singleCellTK, SingleR, singscore, SNPhood, spacexr, spARI, sparrow, SpectralTAD, spicyR, splatter, 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, VDJdive, velociraptor, vmrseq, waddR, weitrix, xCell2, zinbwave, CytoMethIC, IHWpaper, JohnsonKinaseData, seqpac, causalBatch, DCLEAR, DTSEA, DysPIA, enviGCMS, GSEMA, Holomics, LDM, minSNPs, oosse, robin, scGate, spatialGE

Links To Me

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

Source Package BiocParallel_1.45.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) BiocParallel_1.45.0.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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