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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