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
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PDF
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R Script
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Efficient genome searching with Biostrings and the BSgenome data packages |
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PDF
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R Script
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How to forge a BSgenome data package |
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PDF
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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 |
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| License |
Artistic-2.0 |
| URL |
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| 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
