To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome")

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

BSgenome

Infrastructure for Biostrings-based genome data packages

Bioconductor version: Release (2.14)

Infrastructure shared by all the Biostrings-based genome data packages

Author: Herve Pages

Maintainer: H. Pages <hpages at fhcrc.org>

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

Installation

To install this package, start R and enter:

source("http://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 1.32.0
In Bioconductor since BioC 1.9 (R-2.4)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.1.2), IRanges(>= 1.13.6), GenomicRanges(>= 1.15.9), Biostrings(>= 2.23.3)
Imports methods, BiocGenerics, IRanges, GenomicRanges, XVector, Biostrings, Rsamtools
Suggests BiocInstaller, BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19.masked, SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase, GenomeInfoDb, RUnit
System Requirements
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.Celegans.UCSC.ce10, 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.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.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.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, 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.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, 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, CAGEr, chipseq, cleanUpdTSeq, CRISPRseek, GenomicAlignments, GOTHiC, htSeqTools, leeBamViews, MEDIPS, motifRG, REDseq, rGADEM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608
Imports Me 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.Celegans.UCSC.ce10, 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.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.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.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, 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.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, 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, charm, ChIPpeakAnno, chipseq, cobindR, ggbio, girafe, gmapR, Gviz, MEDIPS, MethylSeekR, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19, PING, QuasR, R453Plus1Toolbox, Repitools, rtracklayer, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, TFBSTools, VariantAnnotation, VariantFiltering
Suggests Me Biostrings, biovizBase, easyRNASeq, GeneRegionScan, GenomeInfoDb, GenomicFeatures, GenomicRanges, genoset, MEDIPS, MiRaGE, oneChannelGUI, QDNAseq, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, spliceR, waveTiling

Package Archives

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

Package Source BSgenome_1.32.0.tar.gz
Windows Binary BSgenome_1.32.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BSgenome_1.32.0.tgz
Mac OS X 10.9 (Mavericks) BSgenome_1.32.0.tgz
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