BiocParallel

DOI: 10.18129/B9.bioc.BiocParallel    

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

Bioconductor facilities for parallel evaluation

Bioconductor version: Development (3.16)

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]

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

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

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews Infrastructure, Software
Version 1.31.12
In Bioconductor since BioC 2.13 (R-3.0) (9 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, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table
SystemRequirements C++11
Enhances
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, cellbaseR, CellBench, CelliD, CellMixS, censcyt, Cepo, ChIPexoQual, ChromSCape, chromswitch, chromVAR, CNVMetrics, CNVRanger, CoGAPS, comapr, coMethDMR, condiments, consensusDE, consICA, contiBAIT, CoreGx, coseq, cpvSNP, CrispRVariants, csaw, CTSV, cydar, CytoGLMM, cytoKernel, cytomapper, dasper, dcGSA, debCAM, DEComplexDisease, DepInfeR, derfinder, DEScan2, DESeq2, DEsingle, DiffBind, Dino, dmrseq, DOSE, DRIMSeq, DropletUtils, Dune, easier, easyRNASeq, EMDomics, enhancerHomologSearch, epimutacions, erma, ERSSA, escape, EWCE, exomePeak2, ExpHunterSuite, factR, fgsea, FindIT2, flowcatchR, flowSpecs, GDCRNATools, GENESIS, GenomAutomorphism, GenomicAlignments, genotypeeval, gmapR, GRaNIE, gscreend, GSEABenchmarkeR, GSVA, h5vc, HiCBricks, HiCcompare, HiCDOC, HTSeqGenie, HTSFilter, iasva, icetea, ideal, IHWpaper, IMAS, imcRtools, IntEREst, IONiseR, IPO, ISAnalytics, IVAS, katdetectr, KinSwingR, LineagePulse, lisaClust, loci2path, LowMACA, LRcell, Macarron, MACPET, mbkmeans, MCbiclust, MetaboAnnotation, metabomxtr, metaseqR2, MethCP, MethylAid, methylGSA, methylInheritance, methylscaper, MetNet, mia, miaViz, microbiomeMarker, MIGSA, miloR, minfi, mixOmics, MMAPPR2, MOGAMUN, monaLisa, motifbreakR, MPRAnalyze, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MSnbase, msqrob2, MSstatsSampleSize, multiHiCcompare, mumosa, muscat, NBAMSeq, NBSplice, nnSVG, NPARC, NxtIRFcore, OmicsLonDA, ORFik, OVESEG, PAIRADISE, 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, scater, scClassify, scDblFinder, scDD, scDDboost, scde, SCFA, scHOT, scMerge, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, scruff, scShapes, scTHI, scuttle, seqArchR, sesame, SEtools, sigFeature, signatureSearch, SimBu, singleCellTK, SingleR, singscore, SNPhood, soGGi, sparrow, spatialHeatmap, SpectralTAD, spicyR, splatter, SpliceWiz, SplicingGraphs, srnadiff, sSNAPPY, STdeconvolve, SUITOR, TAPseq, TarSeqQC, TBSignatureProfiler, ternarynet, TFBSTools, TMixClust, ToxicoGx, TPP2D, tradeSeq, TraRe, TreeSummarizedExperiment, Trendy, TVTB, txcutr, UCell, VariantFiltering, VariantTools, VDJdive, velociraptor, waddR, weitrix, zinbwave
Suggests Me beachmat, CAGEWorkflow, DelayedArray, DIAlignR, EpiCompare, GenomicDataCommons, glmGamPoi, HDF5Array, MethylAidData, MungeSumstats, netSmooth, omicsPrint, PureCN, randRotation, RcisTarget, rebook, scGPS, SeqArray, Single.mTEC.Transcriptomes, 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_1.31.12.tar.gz
Windows Binary BiocParallel_1.31.12.zip (64-bit only)
macOS 10.13 (High Sierra) BiocParallel_1.31.12.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocParallel
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocParallel
Package Short Url https://bioconductor.org/packages/BiocParallel/
Package Downloads Report Download Stats

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