BSgenome: Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation

Infrastructure shared by all the Biostrings-based genome data packages.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome")
AuthorHervé Pagès
Bioconductor views Annotation DataRepresentation Genetics Infrastructure SNP SequenceMatching
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version1.44.0

View on Bioconductor

Functions

alphabetFrequency,BSgenomeViews-method Man page
as.character,BSgenomeViews-method Man page
as.data.frame,BSgenomeViews-method Man page
as.list,BSgenome-method Man page
available.genomes Man page
available.SNPs Man page
bsapply Man page
BSgenome Man page
BSgenome Man page
BSgenome-class Man page
BSgenomeDataPkgSeed Man page
BSgenomeDataPkgSeed-class Man page
BSgenomeForge Man page
[[,BSgenome-method Man page
$,BSgenome-method Man page
BSgenome-utils Man page
BSgenomeViews Man page
BSgenomeViews-class Man page
BSParams Man page
BSParams-class Man page
class:BSgenome Man page
class:BSgenomeDataPkgSeed Man page
class:BSgenomeViews Man page
class:BSParams Man page
class:InjectSNPsHandler Man page
class:ODLT_SNPlocs Man page
class:OldFashionSNPlocs Man page
class:SNPlocs Man page
class:XtraSNPlocs Man page
coerce,BSgenomeViews,DNAStringSet-method Man page
coerce,BSgenomeViews,XStringSet-method Man page
colnames,XtraSNPlocs-method Man page
commonName,SNPlocs-method Man page
commonName,XtraSNPlocs-method Man page
compatibleGenomes Man page
compatibleGenomes,SNPlocs-method Man page
consensusMatrix,BSgenomeViews-method Man page
consensusString,BSgenomeViews-method Man page
countPWM,BSgenome-method Man page
dim,XtraSNPlocs-method Man page
elementNROWS,BSgenomeViews-method Man page
end,BSgenomeViews-method Man page
export,BSgenome,FastaFile,ANY-method Man page
export,BSgenome,TwoBitFile,ANY-method Man page
export-methods Man page
extractROWS,BSgenomeViews-method Man page
forgeBSgenomeDataPkg Man page
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method Man page
forgeBSgenomeDataPkg,character-method Man page
forgeBSgenomeDataPkg,list-method Man page
forgeMasksFiles Man page
forgeSeqFiles Man page
forgeSeqlengthsFile Man page
getBSgenome Man page
getListElement,BSgenomeViews-method Man page
getSeq Man page
getSeq,BSgenome-method Man page
getSeq,XStringSet-method Man page
granges,BSgenomeViews-method Man page
hasOnlyBaseLetters,BSgenomeViews-method Man page
injectSNPs Man page
injectSNPs,BSgenome-method Man page
InjectSNPsHandler Man page
InjectSNPsHandler-class Man page
installed.genomes Man page
installed.SNPs Man page
length,BSgenome-method Man page
length,BSgenomeViews-method Man page
letterFrequency,BSgenomeViews-method Man page
masknames Man page
masknames,BSgenome-method Man page
matchPWM,BSgenome-method Man page
mseqnames Man page
mseqnames,BSgenome-method Man page
names,BSgenome-method Man page
names,BSgenomeViews-method Man page
nchar,BSgenomeViews-method Man page
new_ODLT_SNPlocs Man page
newSNPlocs Man page
newXtraSNPlocs Man page
nucleotideFrequencyAt,BSgenomeViews-method Man page
ODLT_SNPlocs Man page
ODLT_SNPlocs-class Man page
OldFashionSNPlocs Man page
OldFashionSNPlocs-class Man page
oligonucleotideFrequency,BSgenomeViews-method Man page
organism,SNPlocs-method Man page
organism,XtraSNPlocs-method Man page
provider,SNPlocs-method Man page
providerVersion,SNPlocs-method Man page
providerVersion,XtraSNPlocs-method Man page
provider,XtraSNPlocs-method Man page
ranges,BSgenomeViews-method Man page
referenceGenome Man page
referenceGenome,SNPlocs-method Man page
referenceGenome,XtraSNPlocs-method Man page
releaseDate,SNPlocs-method Man page
releaseDate,XtraSNPlocs-method Man page
releaseName,SNPlocs-method Man page
releaseName,XtraSNPlocs-method Man page
seqinfo<-,BSgenome-method Man page
seqinfo,BSgenome-method Man page
seqinfo,BSgenomeViews-method Man page
seqinfo,SNPlocs-method Man page
seqinfo,XtraSNPlocs-method Man page
seqnames<-,BSgenome-method Man page
seqnames,BSgenomeViews-method Man page
seqnames,SNPlocs-method Man page
seqnames,XtraSNPlocs-method Man page
seqtype,BSgenomeViews-method Man page
show,BSgenome-method Man page
show,BSgenomeViews-method Man page
show,SNPlocs-method Man page
show,XtraSNPlocs-method Man page
snpcount Man page
snpcount,BSgenome-method Man page
snpcount,InjectSNPsHandler-method Man page
snpcount,ODLT_SNPlocs-method Man page
snpcount,OldFashionSNPlocs-method Man page
snpcount,SNPlocs-method Man page
snpcount,XtraSNPlocs-method Man page
snpid2alleles Man page
snpid2alleles,OldFashionSNPlocs-method Man page
snpid2alleles,SNPlocs-method Man page
snpid2grange Man page
snpid2grange,OldFashionSNPlocs-method Man page
snpid2grange,SNPlocs-method Man page
snpid2loc Man page
snpid2loc,OldFashionSNPlocs-method Man page
snpid2loc,SNPlocs-method Man page
snplocs Man page
SNPlocs Man page
snplocs,BSgenome-method Man page
SNPlocs-class Man page
snplocs,InjectSNPsHandler-method Man page
snplocs,ODLT_SNPlocs-method Man page
snplocs,OldFashionSNPlocs-method Man page
SNPlocs_pkgname Man page
SNPlocs_pkgname,BSgenome-method Man page
SNPlocs_pkgname,InjectSNPsHandler-method Man page
snplocs,SNPlocs-method Man page
snpsById Man page
snpsById,ODLT_SNPlocs-method Man page
snpsById,OldFashionSNPlocs-method Man page
snpsById,SNPlocs-method Man page
snpsById,XtraSNPlocs-method Man page
snpsByOverlaps Man page
snpsByOverlaps,ODLT_SNPlocs-method Man page
snpsByOverlaps,OldFashionSNPlocs-method Man page
snpsByOverlaps,SNPlocs-method Man page
snpsByOverlaps,XtraSNPlocs-method Man page
snpsBySeqname Man page
snpsBySeqname,ODLT_SNPlocs-method Man page
snpsBySeqname,OldFashionSNPlocs-method Man page
snpsBySeqname,SNPlocs-method Man page
snpsBySeqname,XtraSNPlocs-method Man page
sourceUrl Man page
sourceUrl,BSgenome-method Man page
species,XtraSNPlocs-method Man page
start,BSgenomeViews-method Man page
strand,BSgenomeViews-method Man page
subject,BSgenomeViews-method Man page
uniqueLetters,BSgenomeViews-method Man page
unlist,BSgenomeViews-method Man page
vcountPattern,BSgenome-method Man page
vcountPDict,BSgenome-method Man page
Views,BSgenome-method Man page
vmatchPattern,BSgenome-method Man page
vmatchPDict,BSgenome-method Man page
width,BSgenomeViews-method Man page
writeBSgenomeToFasta Man page
writeBSgenomeToTwobit Man page
[,XStringSet,GenomicRanges-method Man page
[,XStringSet,GRangesList-method Man page
XtraSNPlocs Man page
XtraSNPlocs-class Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BSgenome-class.R R/BSgenome-utils.R R/BSgenomeForge.R R/BSgenomeViews-class.R R/InjectSNPsHandler-class.R R/ODLT_SNPlocs-class.R R/OldFashionSNPlocs-class.R R/OnDiskLongTable-class.R R/OnDiskLongTable_old-class.R R/OnDiskNamedSequences-class.R R/SNPlocs-class.R R/XtraSNPlocs-class.R R/available.genomes.R R/bsapply.R R/export-methods.R R/getSeq-methods.R R/injectSNPs.R R/utils.R
TODO
build
build/vignette.rds
inst
inst/doc
inst/doc/BSgenomeForge.R
inst/doc/BSgenomeForge.Rnw
inst/doc/BSgenomeForge.pdf
inst/doc/GenomeSearching.R
inst/doc/GenomeSearching.Rnw
inst/doc/GenomeSearching.pdf
inst/extdata
inst/extdata/GentlemanLab
inst/extdata/GentlemanLab/1000genomes
inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-seed
inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools
inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools/split_human_b36_female.sh
inst/extdata/GentlemanLab/BSgenome.Amellifera.BeeBase.assembly4-seed
inst/extdata/GentlemanLab/BSgenome.Amellifera.BeeBase.assembly4-tools
inst/extdata/GentlemanLab/BSgenome.Amellifera.BeeBase.assembly4-tools/NOTES.TXT
inst/extdata/GentlemanLab/BSgenome.Amellifera.BeeBase.assembly4-tools/splitbigfasta.sh
inst/extdata/GentlemanLab/BSgenome.Amellifera.UCSC.apiMel2-seed
inst/extdata/GentlemanLab/BSgenome.Amellifera.UCSC.apiMel2.masked-seed
inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.04232008-seed
inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR9-seed
inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR9-tools
inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR9-tools/NOTES.TXT
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau3-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau4-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau4.masked-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau6-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau6-tools
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau6-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau6.masked-seed
inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau8-seed
inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce10-seed
inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce11-seed
inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce2-seed
inst/extdata/GentlemanLab/BSgenome.Celegans.UCSC.ce6-seed
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam2-seed
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam2.masked-seed
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam3-seed
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam3-tools
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam3-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Cfamiliaris.UCSC.canFam3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm2-seed
inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm2.masked-seed
inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm3-seed
inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Dmelanogaster.UCSC.dm6-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer10-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer10-tools
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer10-tools/sort_danRer10.2bit.R
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5-tools
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5-tools/NOTES.TXT
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5-tools/splitbigfasta.sh
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer5.masked-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6-tools
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6-tools/NOTES.TXT
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer6.masked-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7-seed
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7-tools
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7-tools/NOTES.TXT
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Drerio.UCSC.danRer7.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ecoli.NCBI.20080805-seed
inst/extdata/GentlemanLab/BSgenome.Gaculeatus.UCSC.gasAcu1-seed
inst/extdata/GentlemanLab/BSgenome.Gaculeatus.UCSC.gasAcu1.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal3-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal4-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal4-tools
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal4-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal4.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal5-seed
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal5-tools
inst/extdata/GentlemanLab/BSgenome.Ggallus.UCSC.galGal5-tools/sort_galGal5.2bit.R
inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.GRCh38-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.GRCh38-tools
inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.GRCh38-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg17-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg17.masked-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg18-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg18.masked-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg19-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg19.masked-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg38-seed
inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg38.masked-seed
inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.5.0-seed
inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.5.0-tools
inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.5.0-tools/fasta_to_sorted2bit.R
inst/extdata/GentlemanLab/BSgenome.Mfuro.UCSC.musFur1-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac2-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac2.masked-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac3-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac3-tools
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac3-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac8-seed
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac8-tools
inst/extdata/GentlemanLab/BSgenome.Mmulatta.UCSC.rheMac8-tools/sort_rheMac8.2bit.R
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm10-seed
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm10.masked-seed
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm8-seed
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm8.masked-seed
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm9-seed
inst/extdata/GentlemanLab/BSgenome.Mmusculus.UCSC.mm9.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro2-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro2.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro3-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro3-tools
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro3-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro5-seed
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro5-tools
inst/extdata/GentlemanLab/BSgenome.Ptroglodytes.UCSC.panTro5-tools/sort_panTro5.2bit.R
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn4-seed
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn4.masked-seed
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn5-seed
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn5-tools
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn5-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn5.masked-seed
inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn6-seed
inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer1-seed
inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer2-seed
inst/extdata/GentlemanLab/BSgenome.Scerevisiae.UCSC.sacCer3-seed
inst/extdata/GentlemanLab/BSgenome.Sscrofa.UCSC.susScr3-seed
inst/extdata/GentlemanLab/BSgenome.Sscrofa.UCSC.susScr3-tools
inst/extdata/GentlemanLab/BSgenome.Sscrofa.UCSC.susScr3-tools/splitbigfasta.R
inst/extdata/GentlemanLab/BSgenome.Sscrofa.UCSC.susScr3.masked-seed
inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut1-seed
inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut1.masked-seed
inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut2-seed
inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut2-tools
inst/extdata/GentlemanLab/BSgenome.Tguttata.UCSC.taeGut2-tools/sort_taeGut2.2bit.R
inst/extdata/GentlemanLab/BSgenome.influenza.NCBI.20100628-seed
inst/extdata/GentlemanLab/ForgeAll.R
inst/extdata/GentlemanLab/bump_seed_version.sh
inst/extdata/ce2chrM.fa.gz
inst/extdata/ce2chrX.fa.gz
inst/extdata/ce2dict0.fa
inst/pkgtemplates
inst/pkgtemplates/BSgenome_datapkg
inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
inst/pkgtemplates/BSgenome_datapkg/NAMESPACE
inst/pkgtemplates/BSgenome_datapkg/R
inst/pkgtemplates/BSgenome_datapkg/R/zzz.R
inst/pkgtemplates/BSgenome_datapkg/inst
inst/pkgtemplates/BSgenome_datapkg/inst/extdata
inst/pkgtemplates/BSgenome_datapkg/man
inst/pkgtemplates/BSgenome_datapkg/man/package.Rd
inst/pkgtemplates/MaskedBSgenome_datapkg
inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
inst/pkgtemplates/MaskedBSgenome_datapkg/NAMESPACE
inst/pkgtemplates/MaskedBSgenome_datapkg/R
inst/pkgtemplates/MaskedBSgenome_datapkg/R/zzz.R
inst/pkgtemplates/MaskedBSgenome_datapkg/inst
inst/pkgtemplates/MaskedBSgenome_datapkg/inst/extdata
inst/pkgtemplates/MaskedBSgenome_datapkg/man
inst/pkgtemplates/MaskedBSgenome_datapkg/man/package.Rd
man
man/BSParams-class.Rd man/BSgenome-class.Rd man/BSgenome-utils.Rd man/BSgenomeForge.Rd man/BSgenomeViews-class.Rd man/SNPlocs-class.Rd man/XtraSNPlocs-class.Rd man/available.genomes.Rd man/bsapply.Rd man/export-methods.Rd man/getSeq-methods.Rd man/injectSNPs.Rd
tests
vignettes
vignettes/BSgenomeForge.Rnw
vignettes/GenomeSearching.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.