BSgenome

Infrastructure for Biostrings-based genome data packages

Bioconductor version: 2.7

Infrastructure shared by all the Biostrings-based genome data packages

Author: Herve Pages

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

 citation("BSgenome")

Documentation

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

Details

biocViews Genetics, Infrastructure, DataRepresentation, SequenceMatching, Annotation, SNP
Depends R (>= 2.8.0), methods, IRanges(>= 1.7.7), GenomicRanges(>= 0.0.9), Biostrings(>= 2.17.5)
Imports
Suggests RUnit, BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19(>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase
System Requirements
License Artistic-2.0
URL
Depends On Me BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Athaliana.TAIR.01222004, 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.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, ChIPpeakAnno, chipseq, leeBamViews, MEDIPS, PICS, rGADEM
Imports Me BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Athaliana.TAIR.01222004, 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.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, charm, ChIPpeakAnno, chipseq, girafe, MEDIPS, PICS, R453Plus1Toolbox, rtracklayer
Suggests Me Biostrings, GeneRegionScan, GenomicFeatures, GenomicRanges, MEDIPS, oneChannelGUI, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Version 1.18.3
Since Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source BSgenome_1.18.3.tar.gz
Windows Binary BSgenome_1.18.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary BSgenome_1.18.3.tgz
Package Downloads Report Download Stats

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