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  "Package": "BSgenome",
  "Title": "Software infrastructure for efficient representation of full\ngenomes and their SNPs",
  "Description": "Infrastructure shared by all the Biostrings-based genome\ndata packages.",
  "biocViews": "Genetics, Infrastructure, DataRepresentation,\nSequenceMatching, Annotation, SNP",
  "URL": "https://bioconductor.org/packages/BSgenome",
  "BugReports": "https://github.com/Bioconductor/BSgenome/issues",
  "Version": "1.81.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\")",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:48 UTC",
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    "BSgenomeViews",
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    "consensusMatrix",
    "consensusString",
    "countPWM",
    "elementNROWS",
    "end",
    "export",
    "extractAt",
    "forgeBSgenomeDataPkg",
    "forgeMaskedBSgenomeDataPkg",
    "forgeMasksFiles",
    "forgeSeqFiles",
    "forgeSeqlengthsRdaFile",
    "forgeSeqlengthsRdsFile",
    "getBatchesByOverlapsFromOnDiskLongTable",
    "getBatchesBySeqnameFromOnDiskLongTable",
    "getBatchesFromOnDiskLongTable",
    "getBatchesFromOnDiskLongTable_old",
    "getBSgenome",
    "getRowsByIdFromOnDiskLongTable",
    "getRowsByIndexFromOnDiskLongTable_old",
    "getRowsFromOnDiskLongTable",
    "getSeq",
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    "hasOnlyBaseLetters",
    "inferRefAndAltAlleles",
    "injectSNPs",
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    "installed.SNPs",
    "letterFrequency",
    "MaskedBSgenome",
    "masknames",
    "matchPWM",
    "mseqnames",
    "nchar",
    "newSNPlocs",
    "newXtraSNPlocs",
    "nucleotideFrequencyAt",
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    "OnDiskLongTable",
    "OnDiskLongTable_old",
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    "ranges",
    "referenceGenome",
    "releaseDate",
    "releaseName",
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    "saveRowidsForOnDiskLongTable_old",
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    "snplocs",
    "SNPlocs_pkgname",
    "snpsById",
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    "snpsBySeqname",
    "sourceUrl",
    "spatialIndex",
    "start",
    "strand",
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    "uniqueLetters",
    "vcountPattern",
    "Views",
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    "width",
    "writeBSgenomeToFasta",
    "writeBSgenomeToTwobit",
    "writeOnDiskLongTable",
    "writeOnDiskLongTableRowids"
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      "page": "AdvancedBSgenomeForge",
      "title": "[Moved to BSgenomeForge] Tools to forge a BSgenome data package",
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        "forgeBSgenomeDataPkg",
        "forgeMaskedBSgenomeDataPkg",
        "forgeMasksFiles",
        "forgeSeqFiles",
        "forgeSeqlengthsRdaFile",
        "forgeSeqlengthsRdsFile"
      ]
    },
    {
      "page": "available.genomes",
      "title": "Find available/installed genomes",
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        "getBSgenome",
        "installed.genomes"
      ]
    },
    {
      "page": "bsapply",
      "title": "bsapply",
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    },
    {
      "page": "BSgenome-class",
      "title": "BSgenome objects",
      "topics": [
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        "as.list,BSgenome-method",
        "BSgenome",
        "BSgenome-class",
        "bsgenomeName,BSgenome-method",
        "class:BSgenome",
        "coerce,BSgenome,GenomeDescription-method",
        "commonName,BSgenome-method",
        "length,BSgenome-method",
        "masknames",
        "masknames,BSgenome-method",
        "masknames,MaskedBSgenome-method",
        "mseqnames",
        "mseqnames,BSgenome-method",
        "names,BSgenome-method",
        "organism,BSgenome-method",
        "provider,BSgenome-method",
        "providerVersion,BSgenome-method",
        "releaseDate,BSgenome-method",
        "seqinfo,BSgenome-method",
        "seqinfo<-,BSgenome-method",
        "seqnames,BSgenome-method",
        "seqnames<-,BSgenome-method",
        "show,BSgenome-method",
        "sourceUrl",
        "sourceUrl,BSgenome-method",
        "[[,BSgenome-method"
      ]
    },
    {
      "page": "BSgenome-utils",
      "title": "BSgenome utilities",
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        "countPWM,BSgenome-method",
        "matchPWM,BSgenome-method",
        "vcountPattern,BSgenome-method",
        "vcountPDict,BSgenome-method",
        "vmatchPattern,BSgenome-method",
        "vmatchPDict,BSgenome-method"
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    },
    {
      "page": "BSgenomeViews-class",
      "title": "BSgenomeViews objects",
      "topics": [
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        "as.character,BSgenomeViews-method",
        "as.data.frame,BSgenomeViews-method",
        "BSgenomeViews",
        "BSgenomeViews-class",
        "class:BSgenomeViews",
        "coerce,BSgenomeViews,DNAStringSet-method",
        "coerce,BSgenomeViews,XStringSet-method",
        "consensusMatrix,BSgenomeViews-method",
        "consensusString,BSgenomeViews-method",
        "elementNROWS,BSgenomeViews-method",
        "end,BSgenomeViews-method",
        "extractROWS,BSgenomeViews-method",
        "getListElement,BSgenomeViews-method",
        "granges,BSgenomeViews-method",
        "hasOnlyBaseLetters,BSgenomeViews-method",
        "length,BSgenomeViews-method",
        "letterFrequency,BSgenomeViews-method",
        "names,BSgenomeViews-method",
        "nchar,BSgenomeViews-method",
        "nucleotideFrequencyAt,BSgenomeViews-method",
        "oligonucleotideFrequency,BSgenomeViews-method",
        "ranges,BSgenomeViews-method",
        "seqinfo,BSgenomeViews-method",
        "seqnames,BSgenomeViews-method",
        "seqtype,BSgenomeViews-method",
        "show,BSgenomeViews-method",
        "start,BSgenomeViews-method",
        "strand,BSgenomeViews-method",
        "subject,BSgenomeViews-method",
        "uniqueLetters,BSgenomeViews-method",
        "unlist,BSgenomeViews-method",
        "Views,BSgenome-method",
        "width,BSgenomeViews-method"
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    },
    {
      "page": "BSParams-class",
      "title": "Class \"BSParams\"",
      "topics": [
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        "BSParams-class",
        "class:BSParams"
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    },
    {
      "page": "export-methods",
      "title": "Export a BSgenome object as a FASTA or twoBit file",
      "topics": [
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        "export,BSgenome,TwoBitFile,ANY-method",
        "export-methods",
        "writeBSgenomeToFasta",
        "writeBSgenomeToTwobit"
      ]
    },
    {
      "page": "getSeq-methods",
      "title": "getSeq methods for BSgenome and XStringSet objects",
      "topics": [
        "getSeq",
        "getSeq,BSgenome-method",
        "getSeq,XStringSet-method",
        "[,XStringSet,GenomicRanges-method",
        "[,XStringSet,GRangesList-method"
      ]
    },
    {
      "page": "injectSNPs",
      "title": "SNP injection",
      "topics": [
        "available.SNPs",
        "class:InjectSNPsHandler",
        "injectSNPs",
        "injectSNPs,BSgenome-method",
        "InjectSNPsHandler",
        "InjectSNPsHandler-class",
        "installed.SNPs",
        "snpcount,BSgenome-method",
        "snpcount,InjectSNPsHandler-method",
        "snplocs,BSgenome-method",
        "snplocs,InjectSNPsHandler-method",
        "SNPlocs_pkgname",
        "SNPlocs_pkgname,BSgenome-method",
        "SNPlocs_pkgname,InjectSNPsHandler-method"
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    },
    {
      "page": "SNPlocs-class",
      "title": "SNPlocs objects",
      "topics": [
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        "class:OldFashionSNPlocs",
        "class:SNPlocs",
        "commonName,SNPlocs-method",
        "compatibleGenomes",
        "compatibleGenomes,SNPlocs-method",
        "inferRefAndAltAlleles",
        "newSNPlocs",
        "new_ODLT_SNPlocs",
        "ODLT_SNPlocs",
        "ODLT_SNPlocs-class",
        "OldFashionSNPlocs",
        "OldFashionSNPlocs-class",
        "organism,SNPlocs-method",
        "provider,SNPlocs-method",
        "providerVersion,SNPlocs-method",
        "referenceGenome",
        "referenceGenome,SNPlocs-method",
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        "releaseName",
        "releaseName,SNPlocs-method",
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        "seqnames,SNPlocs-method",
        "show,SNPlocs-method",
        "snpcount",
        "snpcount,ODLT_SNPlocs-method",
        "snpcount,OldFashionSNPlocs-method",
        "snpcount,SNPlocs-method",
        "SNPlocs",
        "snplocs",
        "snplocs,ODLT_SNPlocs-method",
        "snplocs,OldFashionSNPlocs-method",
        "snplocs,SNPlocs-method",
        "SNPlocs-class",
        "snpsById",
        "snpsById,ODLT_SNPlocs-method",
        "snpsById,OldFashionSNPlocs-method",
        "snpsById,SNPlocs-method",
        "snpsByOverlaps",
        "snpsByOverlaps,ODLT_SNPlocs-method",
        "snpsByOverlaps,OldFashionSNPlocs-method",
        "snpsByOverlaps,SNPlocs-method",
        "snpsBySeqname",
        "snpsBySeqname,ODLT_SNPlocs-method",
        "snpsBySeqname,OldFashionSNPlocs-method",
        "snpsBySeqname,SNPlocs-method"
      ]
    },
    {
      "page": "XtraSNPlocs-class",
      "title": "XtraSNPlocs objects",
      "topics": [
        "class:XtraSNPlocs",
        "colnames,XtraSNPlocs-method",
        "commonName,XtraSNPlocs-method",
        "dim,XtraSNPlocs-method",
        "newXtraSNPlocs",
        "organism,XtraSNPlocs-method",
        "provider,XtraSNPlocs-method",
        "providerVersion,XtraSNPlocs-method",
        "referenceGenome,XtraSNPlocs-method",
        "releaseDate,XtraSNPlocs-method",
        "releaseName,XtraSNPlocs-method",
        "seqinfo,XtraSNPlocs-method",
        "seqnames,XtraSNPlocs-method",
        "show,XtraSNPlocs-method",
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        "snpsById,XtraSNPlocs-method",
        "snpsByOverlaps,XtraSNPlocs-method",
        "snpsBySeqname,XtraSNPlocs-method",
        "species,XtraSNPlocs-method",
        "XtraSNPlocs",
        "XtraSNPlocs-class"
      ]
    }
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