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 2.10 of Bioconductor; for the stable, up-to-date release version, see BSgenome.

Infrastructure for Biostrings-based genome data packages

Bioconductor version: 2.10

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:

## 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 Efficient genome searching with Biostrings and the BSgenome data packages
PDF How to forge a BSgenome data package
PDF   Reference Manual

Details

biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version 1.24.0
In Bioconductor since BioC 1.9 (R-2.4) (9.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.1.2), IRanges(>= 1.13.6), GenomicRanges(>= 1.7.5), Biostrings(>= 2.23.3)
Imports
LinkingTo
Suggests RUnit, BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19(>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase
SystemRequirements
Enhances
URL
Depends On Me BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer7, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Tgondii.ToxoDB.7.0, ChIPpeakAnno, chipseq, easyRNASeq, htSeqTools, leeBamViews, MEDIPS, PICS, r3Cseq, REDseq, rGADEM
Imports Me BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer7, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Tgondii.ToxoDB.7.0, charm, ChIPpeakAnno, chipseq, genoset, ggbio, girafe, MEDIPS, PICS, PING, R453Plus1Toolbox, Repitools, rtracklayer, VariantAnnotation
Suggests Me Biostrings, biovizBase, GeneRegionScan, GenomicFeatures, GenomicRanges, oneChannelGUI, Repitools, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119
Build Report  

Package Archives

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

Package Source BSgenome_1.24.0.tar.gz
Windows Binary BSgenome_1.24.0.zip
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BSgenome/tree/release-2.10
Package Short Url http://bioconductor.org/packages/BSgenome/
Package Downloads Report Download Stats

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