To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")

In most cases, you don't need to download the package archive at all.

BSgenome

   

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see BSgenome.

Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation

Bioconductor version: 3.4

Infrastructure shared by all the Biostrings-based genome data packages

Author: Hervé Pagès

Maintainer: H. Pagès <hpages at fredhutch.org>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BSgenome")

 

PDF R Script Efficient genome searching with Biostrings and the BSgenome data packages
PDF R Script How to forge a BSgenome data package
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version 1.42.0
In Bioconductor since BioC 1.9 (R-2.4) (10.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.9.36), IRanges(>= 2.1.33), GenomeInfoDb(>= 1.3.19), GenomicRanges(>= 1.23.15), Biostrings(>= 2.35.3), rtracklayer(>= 1.25.8)
Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer
LinkingTo
Suggests BiocInstaller, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, hgu95av2probe, RUnit
SystemRequirements
Enhances
URL
Depends On Me BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, 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.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.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.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.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.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, 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.masked, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, 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.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, 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, CAGEr, cleanUpdTSeq, GOTHiC, HelloRanges, htSeqTools, leeBamViews, MEDIPS, motifRG, REDseq, regioneR, rGADEM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Imports Me AllelicImbalance, BEAT, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, 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.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.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.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.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.Hsapiens.NCBI.GRCh38, 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.masked, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, 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.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, 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, charm, ChIPpeakAnno, cobindR, CRISPRseek, crisprseekplus, diffHic, fitCons.UCSC.hg19, genomation, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, InPAS, MADSEQ, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r0.3.1.nonTCGA.snvs.hs37d5, MafDb.ExAC.r0.3.1.snvs.hs37d5, MethylSeekR, MMDiff2, motifbreakR, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PING, podkat, qsea, QuasR, R453Plus1Toolbox, regioneR, Repitools, seqplots, signeR, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me Biostrings, biovizBase, chipseq, easyRNASeq, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, metaseqR, MiRaGE, MutationalPatterns, oneChannelGUI, QDNAseq, recoup, rtracklayer, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, spliceR, waveTiling
Build Report  

Package Archives

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

Package Source BSgenome_1.42.0.tar.gz
Windows Binary BSgenome_1.42.0.zip
Mac OS X 10.9 (Mavericks) BSgenome_1.42.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BSgenome/tree/release-3.4
Package Short Url http://bioconductor.org/packages/BSgenome/
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