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This is the development version of BSgenome; for the stable release version, see BSgenome.

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

Bioconductor version: Development (3.6)

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

Author: Hervé Pagès

Maintainer: H. Pagès <hpages at>

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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


biocViews Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching, Software
Version 1.45.1
In Bioconductor since BioC 1.9 (R-2.4) (10.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.9.36), IRanges(>= 2.1.33), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.27.6), Biostrings(>= 2.35.3), rtracklayer(>= 1.25.8)
Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer
Suggests BiocInstaller, 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 CAGEr, cleanUpdTSeq, GOTHiC, HelloRanges, htSeqTools, MEDIPS, motifRG, REDseq, regioneR, rGADEM
Imports Me AllelicImbalance, BEAT, charm, ChIPpeakAnno, cobindR, CRISPRseek, crisprseekplus, diffHic, gcapc, genomation, GenomicScores, ggbio, gmapR, GreyListChIP, GUIDEseq, Gviz, hiAnnotator, InPAS, MADSEQ, MethylSeekR, MMDiff2, motifbreakR, PING, podkat, qsea, QuasR, R453Plus1Toolbox, regioneR, REMP, Repitools, signeR, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools
Suggests Me Biostrings, biovizBase, chipseq, easyRNASeq, GeneRegionScan, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, genoset, metaseqR, MiRaGE, MutationalPatterns, oneChannelGUI, QDNAseq, recoup, rtracklayer, spliceR, waveTiling
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