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  "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"Valerie\", \"Obenchain\", role=\"aut\"),\nperson(\"Martin\", \"Morgan\", role=\"aut\"),\nperson(\"Fedor\", \"Bezrukov\", role=\"ctb\"),\nperson(\"Robert\", \"Castelo\", role=\"ctb\"),\nperson(\"Halimat C.\", \"Atanda\", role=\"ctb\",\ncomment=\"Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.\"\n))",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-07 19:01:09 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicAlignments",
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        "findCompatibleOverlaps,GAlignmentPairs,GRangesList-method",
        "findCompatibleOverlaps,GAlignments,GRangesList-method",
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      "title": "Pairing the elements of a GAlignments object",
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        "findMateAlignment",
        "flushDumpedAlignments",
        "getDumpedAlignments",
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        "findOverlaps,GAlignmentPairs,Vector-method",
        "findOverlaps,GAlignments,GAlignments-method",
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        "findSpliceOverlaps,GAlignments,GRangesList-method",
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        "bindROWS,GAlignmentPairs-method",
        "class:GAlignmentPairs",
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        "second,GAlignmentPairs-method",
        "seqinfo,GAlignmentPairs-method",
        "seqinfo<-,GAlignmentPairs-method",
        "seqlevelsInUse,GAlignmentPairs-method",
        "seqnames,GAlignmentPairs-method",
        "show,GAlignmentPairs-method",
        "strand,GAlignmentPairs-method",
        "strandMode",
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        "strandMode<-",
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        "unlist,GAlignmentPairs-method",
        "updateObject,GAlignmentPairs-method",
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      "page": "GAlignments-class",
      "title": "GAlignments objects",
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        "cigar",
        "cigar,GAlignments-method",
        "class:GAlignments",
        "coerce,GAlignments,DataFrame-method",
        "coerce,GAlignments,GRanges-method",
        "coerce,GAlignments,GRangesList-method",
        "coerce,GAlignments,IntegerRanges-method",
        "coerce,GAlignments,IntegerRangesList-method",
        "coerce,GenomicRanges,GAlignments-method",
        "GAlignments",
        "GAlignments-class",
        "getListElement,GAlignments-method",
        "granges,GAlignments-method",
        "grglist,GAlignments-method",
        "is.unsorted,GAlignments-method",
        "names,GAlignments-method",
        "names<-,GAlignments-method",
        "njunc",
        "njunc,GAlignments-method",
        "order,GAlignments-method",
        "parallel_slot_names,GAlignments-method",
        "pcompare,GAlignments,GAlignments-method",
        "qwidth",
        "qwidth,GAlignments-method",
        "ranges,GAlignments-method",
        "rank,GAlignments-method",
        "rglist,GAlignments-method",
        "rname",
        "rname,GAlignments-method",
        "rname<-",
        "rname<-,GAlignments-method",
        "seqinfo,GAlignments-method",
        "seqinfo<-,GAlignments-method",
        "seqnames,GAlignments-method",
        "seqnames<-,GAlignments-method",
        "show,GAlignments-method",
        "sort,GAlignments-method",
        "start,GAlignments-method",
        "strand,GAlignments-method",
        "strand<-,GAlignments,ANY-method",
        "update,GAlignments-method",
        "updateObject,GAlignments-method",
        "width,GAlignments-method"
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    },
    {
      "page": "GAlignmentsList-class",
      "title": "GAlignmentsList objects",
      "topics": [
        "cigar,GAlignmentsList-method",
        "class:GAlignmentsList",
        "coerce,GAlignmentPairs,GAlignmentsList-method",
        "coerce,GAlignmentsList,GAlignmentPairs-method",
        "coerce,GAlignmentsList,GRanges-method",
        "coerce,GAlignmentsList,GRangesList-method",
        "coerce,GAlignmentsList,IntegerRanges-method",
        "coerce,GAlignmentsList,IntegerRangesList-method",
        "coerce,list,GAlignmentsList-method",
        "elementMetadata,GAlignmentsList-method",
        "elementMetadata<-,GAlignmentsList-method",
        "GAlignmentsList",
        "GAlignmentsList-class",
        "granges,GAlignmentsList-method",
        "grglist,GAlignmentsList-method",
        "names,GAlignmentsList-method",
        "names<-,GAlignmentsList-method",
        "njunc,GAlignmentsList-method",
        "qwidth,GAlignmentsList-method",
        "ranges,GAlignmentsList-method",
        "relistToClass,GAlignments-method",
        "rglist,GAlignmentsList-method",
        "rname,GAlignmentsList-method",
        "rname<-,GAlignmentsList-method",
        "seqinfo,GAlignmentsList-method",
        "seqinfo<-,GAlignmentsList-method",
        "seqnames,GAlignmentsList-method",
        "seqnames<-,GAlignmentsList-method",
        "show,GAlignmentsList-method",
        "strand,GAlignmentsList-method",
        "strand<-,GAlignmentsList,character-method",
        "strand<-,GAlignmentsList-method"
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      "page": "GappedReads-class",
      "title": "(Legacy) GappedReads objects",
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        "class:GappedReads",
        "GappedReads",
        "GappedReads-class",
        "qseq",
        "qseq,GappedReads-method",
        "qwidth,GappedReads-method"
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    },
    {
      "page": "intra-range-methods",
      "title": "Intra range transformations of a GAlignments or GAlignmentsList object",
      "topics": [
        "intra-range-methods",
        "narrow,GappedReads-method",
        "qnarrow",
        "qnarrow,GAlignments-method",
        "qnarrow,GAlignmentsList-method",
        "qnarrow,GappedReads-method",
        "windows,GAlignments-method"
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    },
    {
      "page": "junctions-methods",
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      "topics": [
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        "junctions,GAlignments-method",
        "junctions,GAlignmentsList-method",
        "junctions-methods",
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    },
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      "page": "coordinate-mapping-methods",
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        "OverlapEncodings",
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      "page": "pileLettersAt",
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      "page": "readGAlignments",
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      "page": "sequenceLayer",
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      "page": "setops-methods",
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      "page": "stackStringsFromGAlignments",
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        "summarizeOverlaps,GRangesList,GRanges-method",
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