BSgenome

DOI: 10.18129/B9.bioc.BSgenome    

Software infrastructure for efficient representation of full genomes and their SNPs

Bioconductor version: Release (3.13)

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

Author: Hervé Pagès

Maintainer: H. Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("BSgenome")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BSgenome")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BSgenome")

 

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
Text   NEWS

Details

biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version 1.60.0
In Bioconductor since BioC 1.9 (R-2.4) (15 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.28), IRanges(>= 2.13.16), GenomeInfoDb(>= 1.25.6), GenomicRanges(>= 1.31.10), Biostrings(>= 2.47.6), rtracklayer(>= 1.39.7)
Imports methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector(>= 0.29.3), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer
LinkingTo
Suggests BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
SystemRequirements
Enhances
URL https://bioconductor.org/packages/BSgenome
BugReports https://github.com/Bioconductor/BSgenome/issues
Depends On Me annotation, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.NCBI.AmelHAv3.1, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Aofficinalis.NCBI.V1, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Btaurus.UCSC.bosTau9, BSgenome.Carietinum.NCBI.v1, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Cjacchus.UCSC.calJac3, BSgenome.Creinhardtii.JGI.v5.6, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer11, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Dvirilis.Ensembl.dvircaf1, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Ggallus.UCSC.galGal6, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mdomestica.UCSC.monDom5, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac10, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ppaniscus.UCSC.panPan1, BSgenome.Ppaniscus.UCSC.panPan2, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Ptroglodytes.UCSC.panTro6, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr11, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, ChIPanalyser, GOTHiC, HelloRanges, leeBamViews, MEDIPS, periodicDNA, REDseq, rGADEM, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, VarCon, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Imports Me AllelicImbalance, appreci8R, ATACseqQC, atSNP, BEAT, BSgenome.Alyrata.JGI.v1, BSgenome.Amellifera.BeeBase.assembly4, BSgenome.Amellifera.NCBI.AmelHAv3.1, BSgenome.Amellifera.UCSC.apiMel2, BSgenome.Amellifera.UCSC.apiMel2.masked, BSgenome.Aofficinalis.NCBI.V1, BSgenome.Athaliana.TAIR.04232008, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau3.masked, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau4.masked, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau6.masked, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Btaurus.UCSC.bosTau9, BSgenome.Carietinum.NCBI.v1, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Celegans.UCSC.ce6, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam2.masked, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Cfamiliaris.UCSC.canFam3.masked, BSgenome.Cjacchus.UCSC.calJac3, BSgenome.Creinhardtii.JGI.v5.6, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm2.masked, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm3.masked, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer11, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer5.masked, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer6.masked, BSgenome.Drerio.UCSC.danRer7, BSgenome.Drerio.UCSC.danRer7.masked, BSgenome.Dvirilis.Ensembl.dvircaf1, BSgenome.Ecoli.NCBI.20080805, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Gaculeatus.UCSC.gasAcu1.masked, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal3.masked, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Ggallus.UCSC.galGal4.masked, BSgenome.Ggallus.UCSC.galGal5, BSgenome.Ggallus.UCSC.galGal6, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Hsapiens.UCSC.hg17.masked, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mdomestica.UCSC.monDom5, BSgenome.Mfascicularis.NCBI.5.0, BSgenome.Mfuro.UCSC.musFur1, BSgenome.Mmulatta.UCSC.rheMac10, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac2.masked, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmulatta.UCSC.rheMac3.masked, BSgenome.Mmulatta.UCSC.rheMac8, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Mmusculus.UCSC.mm8.masked, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Osativa.MSU.MSU7, BSgenome.Ppaniscus.UCSC.panPan1, BSgenome.Ppaniscus.UCSC.panPan2, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro2.masked, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Ptroglodytes.UCSC.panTro3.masked, BSgenome.Ptroglodytes.UCSC.panTro5, BSgenome.Ptroglodytes.UCSC.panTro6, BSgenome.Rnorvegicus.UCSC.rn4, BSgenome.Rnorvegicus.UCSC.rn4.masked, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Rnorvegicus.UCSC.rn5.masked, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Sscrofa.UCSC.susScr11, BSgenome.Sscrofa.UCSC.susScr3, BSgenome.Sscrofa.UCSC.susScr3.masked, BSgenome.Tgondii.ToxoDB.7.0, BSgenome.Tguttata.UCSC.taeGut1, BSgenome.Tguttata.UCSC.taeGut1.masked, BSgenome.Tguttata.UCSC.taeGut2, BSgenome.Vvinifera.URGI.IGGP12Xv0, BSgenome.Vvinifera.URGI.IGGP12Xv2, BSgenome.Vvinifera.URGI.IGGP8X, bsseq, BUSpaRse, CAGEr, chromVAR, circRNAprofiler, cleanUpdTSeq, CRISPRseek, crisprseekplus, diffHic, dpeak, enrichTF, esATAC, EventPointer, exomePeak2, fitCons.UCSC.hg19, FRASER, gcapc, genomation, GenomicDistributionsData, GenVisR, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, HiCDCPlus, InPAS, IsoformSwitchAnalyzeR, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomAD.r3.0.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.r3.0.GRCh38, MafH5.gnomAD.v3.1.1.GRCh38, methrix, MethylSeekR, MMDiff2, motifbreakR, motifmatchr, msgbsR, multicrispr, MungeSumstats, musicatk, MutationalPatterns, ORFik, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PING, pipeFrame, podkat, qsea, QuasR, R453Plus1Toolbox, RareVariantVis, RCAS, regioneR, REMP, Repitools, ribosomeProfilingQC, RNAmodR, scmeth, SCOPE, seqplots, SigsPack, SingleMoleculeFootprinting, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, SparseSignatures, TAPseq, TFBSTools, trena, tRNAscanImport, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, XNAString, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me bambu, Biostrings, biovizBase, ChIPpeakAnno, chipseq, easyRNASeq, eisaR, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, maftools, metaseqR2, MiRaGE, PWMEnrich, QDNAseq, recoup, rtracklayer, sitadela, SNPlocs.Hsapiens.dbSNP.20101109
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BSgenome_1.60.0.tar.gz
Windows Binary BSgenome_1.60.0.zip
macOS 10.13 (High Sierra) BSgenome_1.60.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BSgenome
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BSgenome
Package Short Url https://bioconductor.org/packages/BSgenome/
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