BSgenome
Infrastructure for Biostrings-based genome data packages
Bioconductor version: 2.13
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:
source("http://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")
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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 |
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Text
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NEWS |
Details
| biocViews |
Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software |
| Version |
1.30.0 |
| In Bioconductor since |
BioC 1.9 (R-2.4) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.8.0), methods, BiocGenerics(>= 0.1.2), IRanges(>= 1.13.6), GenomicRanges(>= 1.11.46), Biostrings(>= 2.23.3) |
| Imports |
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| 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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| URL |
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| 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.Btaurus.UCSC.bosTau6, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam3, 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.Ggallus.UCSC.galGal4, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Tgondii.ToxoDB.7.0, CAGEr, ChIPpeakAnno, chipseq, cleanUpdTSeq, htSeqTools, leeBamViews, MEDIPS, motifRG, REDseq, rGADEM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608 |
| 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.Btaurus.UCSC.bosTau6, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam3, 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.Ggallus.UCSC.galGal4, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Osativa.MSU.MSU7, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Tgondii.ToxoDB.7.0, charm, ChIPpeakAnno, chipseq, cobindR, ggbio, girafe, gmapR, Gviz, MEDIPS, MethylSeekR, PING, QuasR, R453Plus1Toolbox, Repitools, rtracklayer, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20120608, VariantAnnotation |
| Suggests Me |
Biostrings, biovizBase, easyRNASeq, GeneRegionScan, GenomicFeatures, GenomicRanges, genoset, MEDIPS, MiRaGE, oneChannelGUI, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, spliceR, waveTiling |
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