DOI: 10.18129/B9.bioc.BSgenome    

This is the development version of BSgenome; to use it, please install the devel version of Bioconductor.

Software infrastructure for efficient representation of full genomes and their SNPs

Bioconductor version: Development (3.10)

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

Author: Hervé Pagès

Maintainer: H. Pagès <hpages at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

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


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



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


biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version 1.53.0
In Bioconductor since BioC 1.9 (R-2.4) (12.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.28), IRanges(>= 2.13.16), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.10), Biostrings(>= 2.47.6), rtracklayer(>= 1.39.7)
Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer
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, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
Depends On Me annotation, ChIPanalyser, HelloRanges, leeBamViews, MEDIPS, motifRG, REDseq, rGADEM
Imports Me AllelicImbalance, appreci8R, ATACseqQC, atSNP, BEAT, bsseq, CAGEr, charm, ChIPpeakAnno, chromVAR, cleanUpdTSeq, cobindR, CRISPRseek, crisprseekplus, diffHic, enrichTF, esATAC, EventPointer, gcapc, genomation, GenomicScores, GenVisR, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, InPAS, IsoformSwitchAnalyzeR, MADSEQ, MethylSeekR, MMDiff2, motifbreakR, motifmatchr, msgbsR, PING, pipeFrame, podkat, qsea, QuasR, R453Plus1Toolbox, RareVariantVis, regioneR, REMP, Repitools, scmeth, seqplots, SparseSignatures, TFBSTools, trena, Ularcirc, VariantAnnotation, VariantFiltering, VariantTools
Suggests Me Biostrings, biovizBase, chipseq, easyRNASeq, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, maftools, metaseqR, MiRaGE, MutationalPatterns, ORFik, QDNAseq, recoup, rtracklayer, waveTiling
Links To Me
Build Report  

Package Archives

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

Source Package BSgenome_1.53.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) BSgenome_1.53.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: