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

Infrastructure shared by all the Biostrings-based genome data packages

Author
Hervé Pagès
Date of publication
None
Maintainer
H. Pagès <hpages@fredhutch.org>
License
Artistic-2.0
Version
1.42.0

View on Bioconductor

Man pages

available.genomes
Find available/installed genomes
bsapply
bsapply
BSgenome-class
BSgenome objects
BSgenomeForge
The BSgenomeForge functions
BSgenome-utils
BSgenome utilities
BSgenomeViews-class
BSgenomeViews objects
BSParams-class
Class "BSParams"
export-methods
Export a BSgenome object as a FASTA or twoBit file
getSeq-methods
getSeq methods for BSgenome and XStringSet objects
injectSNPs
SNP injection
SNPlocs-class
SNPlocs objects
XtraSNPlocs-class
XtraSNPlocs objects

Files in this package

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