BSgenome

This is thereleased version of BSgenome; for the devel version, seeBSgenome.

Software infrastructure for efficient representation of full genomes and their SNPs

DOI: 10.18129/B9.bioc.BSgenome

Bioconductor version: Release (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, entercitation("BSgenome")):

Installation

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

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

For older versions of R, please refer to the appropriateBioconductor 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation,DataRepresentation,Genetics,Infrastructure,SNP,SequenceMatching,Software
Version	1.78.0
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(>= 0.47.6),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

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,DMRcaller,enhancerHomologSearch,esATAC,EventPointer,FRASER,gcapc,genomation,ggbio,gmapR,GreyListChIP,GUIDEseq,Gviz,HiCaptuRe,IsoformSwitchAnalyzeR,katdetectr,m6Aboost,methodical,methrix,MethylSeekR,MMDiff2,monaLisa,Motif2Site,motifbreakR,motifmatchr,MotifPeeker,msgbsR,multicrispr,MungeSumstats,musicatk,MutationalPatterns,ORFik,pipeFrame,podkat,qsea,QuasR,raer,RAIDS,RareVariantVis,RCAS,regioneR,REMP,RESOLVE,ribosomeProfilingQC,RNAmodR,scmeth,SCOPE,signeR,SigsPack,SingleMoleculeFootprinting,SparseSignatures,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,GeneRegionScan,GenomeInfoDb,GenomicAlignments,GenomicFeatures,GenomicRanges,maftools,metaseqR2,MiRaGE,PICB,plotgardener,ProteoDisco,PWMEnrich,QDNAseq,recoup,RiboCrypt,rtracklayer,Seqinfo,sitadela,gkmSVM,sigminer,Signac
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	BSgenome_1.78.0.tar.gz
Windows Binary (x86_64)	BSgenome_1.78.0.zip
macOS Binary (x86_64)	BSgenome_1.78.0.tgz
macOS Binary (arm64)	BSgenome_1.78.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BSgenome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BSgenome
Bioc Package Browser	https://code.bioconductor.org/browse/BSgenome/
Package Short Url	https://bioconductor.org/packages/BSgenome/
Package Downloads Report	Download Stats

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