BiocParallel

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BiocParallel.

Bioconductor facilities for parallel evaluation


Bioconductor version: 3.10

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

Author: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Valerie Obenchain [aut], Michel Lang [aut], Ryan Thompson [aut], Nitesh Turaga [aut]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.6") 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 PDF R Script
2. Introduction to BatchtoolsParam PDF R Script
3. Errors, Logs and Debugging PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software
Version 1.20.1
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2 | GPL-3
Depends methods
Imports stats, utils, futile.logger, parallel, snow
System Requirements C++11
URL https://github.com/Bioconductor/BiocParallel
Bug Reports https://github.com/Bioconductor/BiocParallel/issues
See More
Suggests BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table
Linking To BH
Enhances
Depends On Me bacon, BEclear, Cardinal, ClassifyR, clusterSeq, consensusSeekeR, CopywriteR, cydar, deco, DelayedArray, DEWSeq, DEXSeq, DMCFB, DMCHMM, doppelgangR, GenomicFiles, hiReadsProcessor, INSPEcT, matter, MBASED, metagene, metagene2, ncGTW, Oscope, OUTRIDER, PCAN, pRoloc, Rqc, sequencing, ShortRead, SigCheck, STROMA4, SummarizedBenchmark, sva, xcms
Imports Me abseqR, AffiXcan, ALDEx2, AlphaBeta, ALPS, amplican, ASICS, ASpediaFI, atSNP, BANDITS, batchelor, bayNorm, BiocNeighbors, BioCor, BiocSingular, BioMM, BioNetStat, biotmle, brendaDb, bsseq, CAGEfightR, CAGEr, CAMTHC, cellbaseR, CellBench, CellMixS, ChIPexoQual, ChIPQC, chromswitch, chromVAR, CNVRanger, CoGAPS, consensusDE, contiBAIT, coseq, cpvSNP, CRISPRseek, CrispRVariants, csaw, dcGSA, debCAM, DEComplexDisease, DelayedMatrixStats, derfinder, DEScan2, DESeq2, DEsingle, DiffBind, dmrseq, DOSE, DRIMSeq, DropletUtils, easyRNASeq, EMDomics, erma, ERSSA, fgsea, FindMyFriends, flowcatchR, flowSpecs, GDCRNATools, GenoGAM, GenomicAlignments, genotypeeval, gmapR, gscreend, GSEABenchmarkeR, GUIDEseq, h5vc, HiCBricks, HiCcompare, HTSeqGenie, HTSFilter, iasva, icetea, ideal, IHWpaper, IMAS, ImpulseDE2, InPAS, IntEREst, IONiseR, IPO, IVAS, JunctionSeq, KinSwingR, LineagePulse, loci2path, LowMACA, MACPET, MCbiclust, metabomxtr, MethCP, MethylAid, methylGSA, methylInheritance, methyvim, MetNet, MIGSA, minfi, MMAPPR2, motifbreakR, MPRAnalyze, MSnbase, MSstatsSampleSize, multiHiCcompare, muscat, NBAMSeq, NBSplice, OmicsLonDA, ORFik, OVESEG, PAIRADISE, Pbase, PCAtools, PowerExplorer, pram, PrecisionTrialDrawer, proFIA, profileplyr, qpgraph, qsea, QuasR, Rcwl, recount, REMP, RJMCMCNucleosomes, RNAmodR, Rsamtools, RUVcorr, scater, scDblFinder, scDD, scde, scMerge, SCnorm, scone, scoreInvHap, scPCA, scran, scRecover, scruff, sesame, sigFeature, signatureSearch, SingleR, singscore, SNPhood, soGGi, SpectralTAD, splatter, SplicingGraphs, srnadiff, TarSeqQC, TFBSTools, TMixClust, tradeSeq, trena, Trendy, TSRchitect, TVTB, TxRegInfra, variancePartition, VariantFiltering, VariantTools, waddR, zinbwave
Suggests Me CAGEWorkflow, chimera, curatedMetagenomicData, HDF5Array, MethylAidData, netSmooth, omicsPrint, PureCN, RcisTarget, scGPS, SeqArray, systemPipeR, TENxBrainData, TENxPBMCData, TFutils, tofsims, universalmotif
Links To Me
Build Report Build Report

Package Archives

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

Source Package BiocParallel_1.20.1.tar.gz
Windows Binary BiocParallel_1.20.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BiocParallel_1.20.1.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 3.10 Source Archive