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Bioconductor - BSgenome (development version)

BSgenome

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

Software infrastructure for efficient representation of full genomes and their SNPs

Bioconductor version: Development (3.22)

Infrastructure shared by all the Biostrings-based genome data packages.

Author: Hervé Pagès [aut, cre]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("BSgenome")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BSgenome")

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("BSgenome")
Efficient genome searching with Biostrings and the BSgenome data packages PDF R Script How to forge a BSgenome data package PDF Reference Manual PDF NEWS Text Details biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software Version 1.77.1 In Bioconductor since BioC 1.9 (R-2.4) (19 years) License Artistic-2.0 Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.28), IRanges(>= 2.13.16), Seqinfo, GenomicRanges(>= 1.61.1), Biostrings(>= 2.77.2), BiocIO, rtracklayer(>= 1.69.1) Imports utils, stats, matrixStats, XVector, Rsamtools(>= 2.25.1) System Requirements URL https://bioconductor.org/packages/BSgenome Bug Reports https://github.com/Bioconductor/BSgenome/issues See More Suggests BiocManager, GenomeInfoDb, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge Linking To Enhances Depends On Me bambu, BSgenomeForge, ChIPanalyser, GOTHiC, HelloRanges, MEDIPS, periodicDNA, REDseq, VarCon, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.NCBI.AmelHAv3.1, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Aofficinalis.NCBI.V1, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Btaurus.UCSC.bosTau9, BSgenome.Btaurus.UCSC.bosTau9.masked, BSgenome.Carietinum.NCBI.v1, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Cjacchus.UCSC.calJac3, BSgenome.Cjacchus.UCSC.calJac4, BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1, BSgenome.Creinhardtii.JGI.v5.6, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer11, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Dvirilis.Ensembl.dvircaf1, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Ggallus.UCSC.galGal6, BSgenome.Gmax.NCBI.Gmv40, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hs1, BSgenome.Mdomestica.UCSC.monDom5, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfascicularis.NCBI.6.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac10, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ppaniscus.UCSC.panPan1, BSgenome.Ppaniscus.UCSC.panPan2, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Ptroglodytes.UCSC.panTro6, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr11, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, leeBamViews, annotation Imports Me AllelicImbalance, appreci8R, ATACseqQC, atSNP, BEAT, bsseq, BUSpaRse, CAGEr, chromVAR, cleanUpdTSeq, CleanUpRNAseq, cliProfiler, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, crisprViz, diffHic, enhancerHomologSearch, esATAC, EventPointer, FRASER, gcapc, genomation, GenVisR, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, IsoformSwitchAnalyzeR, katdetectr, m6Aboost, methodical, methrix, MethylSeekR, MMDiff2, monaLisa, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, msgbsR, multicrispr, MungeSumstats, musicatk, MutationalPatterns, ORFik, pipeFrame, podkat, qsea, QuasR, R453Plus1Toolbox, raer, RAIDS, RareVariantVis, RCAS, regioneR, REMP, Repitools, RESOLVE, ribosomeProfilingQC, RNAmodR, scmeth, SCOPE, seqArchRplus, signeR, SigsPack, SingleMoleculeFootprinting, SparseSignatures, spatzie, spiky, SpliceWiz, TAPseq, TFBSTools, transmogR, tRNAscanImport, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.NCBI.AmelHAv3.1, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Aofficinalis.NCBI.V1, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Btaurus.UCSC.bosTau9, BSgenome.Btaurus.UCSC.bosTau9.masked, BSgenome.Carietinum.NCBI.v1, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Cjacchus.UCSC.calJac3, BSgenome.Cjacchus.UCSC.calJac4, BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1, BSgenome.Creinhardtii.JGI.v5.6, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer11, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Dvirilis.Ensembl.dvircaf1, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Ggallus.UCSC.galGal6, BSgenome.Gmax.NCBI.Gmv40, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hs1, BSgenome.Mdomestica.UCSC.monDom5, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfascicularis.NCBI.6.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac10, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ppaniscus.UCSC.panPan1, BSgenome.Ppaniscus.UCSC.panPan2, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Ptroglodytes.UCSC.panTro6, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr11, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, fitCons.UCSC.hg19, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v4.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, GenomicDistributionsData, GencoDymo2, ICAMS, revert Suggests Me Biostrings, biovizBase, ChIPpeakAnno, chipseq, DegCre, DiffBind, easyRNASeq, eisaR, factR, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, maftools, metaseqR2, MiRaGE, PICB, plotgardener, ProteoDisco, PWMEnrich, QDNAseq, recoup, RiboCrypt, rtracklayer, Seqinfo, sitadela, gkmSVM, MARVEL, sigminer, Signac Links To Me Build Report Build Report Package Archives

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

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