Bioconductor – BSgenome

Infrastructure for Biostrings-based genome data packages

Bioconductor version: 2.5

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
Depends R (>= 2.7.0), methods, IRanges(>= 1.3.79), Biostrings(>= 2.14.5)
Imports
Suggests BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18(>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20071016, 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.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Celegans.UCSC.ce2, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer5, BSgenome.Ecoli.NCBI.20080805, 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, ShortRead
Imports Me BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Athaliana.TAIR.01222004, BSgenome.Athaliana.TAIR.04232008, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Celegans.UCSC.ce2, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer5, BSgenome.Ecoli.NCBI.20080805, 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, ChIPseqR, GenomicFeatures, rtracklayer, ShortRead
Suggests Me Biostrings, GeneRegionScan, SNPlocs.Hsapiens.dbSNP.20090506
Version 1.14.2
Since Bioconductor 1.9 (R-2.4)

Package Downloads

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