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  "Package": "GenomicRanges",
  "Title": "Representation and manipulation of genomic intervals",
  "Description": "The ability to efficiently represent and manipulate\ngenomic annotations and alignments is playing a central role\nwhen it comes to analyzing high-throughput sequencing data\n(a.k.a. NGS data). The GenomicRanges package defines general\npurpose containers for storing and manipulating genomic\nintervals and variables defined along a genome. More\nspecialized containers for representing and manipulating short\nalignments against a reference genome, or a matrix-like\nsummarization of an experiment, are defined in the\nGenomicAlignments and SummarizedExperiment packages,\nrespectively. Both packages build on top of the GenomicRanges\ninfrastructure.",
  "biocViews": "Genetics, Infrastructure, DataRepresentation, Sequencing,\nAnnotation, GenomeAnnotation, Coverage",
  "URL": "https://bioconductor.org/packages/GenomicRanges",
  "BugReports": "https://github.com/Bioconductor/GenomicRanges/issues",
  "Version": "1.65.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=\"aut\"),\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"Michael\", \"Lawrence\", role=\"aut\"),\nperson(\"Sonali\", \"Arora\", role=\"ctb\"),\nperson(\"Martin\", \"Morgan\", role=\"ctb\"),\nperson(\"Kayla\", \"Morrell\", role=\"ctb\"),\nperson(\"Valerie\", \"Obenchain\", role=\"ctb\"),\nperson(\"Marcel\", \"Ramos\", role=\"ctb\"),\nperson(\"Lori\", \"Shepherd\", role=\"ctb\"),\nperson(\"Dan\", \"Tenenbaum\", role=\"ctb\"),\nperson(\"Daniel\", \"van Twisk\", role=\"ctb\"))",
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  "Collate": "normarg-utils.R utils.R phicoef.R constraint.R strand-utils.R\ngenomic-range-squeezers.R GenomicRanges-class.R\nGenomicRanges-comparison.R GRanges-class.R GPos-class.R\nGRangesFactor-class.R DelegatingGenomicRanges-class.R\nGNCList-class.R GenomicRangesList-class.R GRangesList-class.R\nmakeGRangesFromDataFrame.R makeGRangesListFromDataFrame.R\nRangedData-methods.R findOverlaps-methods.R\nintra-range-methods.R inter-range-methods.R coverage-methods.R\nsetops-methods.R subtract-methods.R nearest-methods.R\nabsoluteRanges.R tileGenome.R tile-methods.R genomicvars.R\nzzz.R",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:30 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicRanges",
  "RemoteRef": "HEAD",
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  "Packaged": {
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  "Author": "Patrick Aboyoun [aut],\nHervé Pagès [aut, cre],\nMichael Lawrence [aut],\nSonali Arora [ctb],\nMartin Morgan [ctb],\nKayla Morrell [ctb],\nValerie Obenchain [ctb],\nMarcel Ramos [ctb],\nLori Shepherd [ctb],\nDan Tenenbaum [ctb],\nDaniel van Twisk [ctb]",
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    "absoluteRanges",
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    "as.factor",
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    "distance",
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    "duplicated",
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    "end<-",
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    "from_GPos_to_GRanges",
    "gaps",
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    "granges",
    "GRanges",
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    "intersect",
    "invertStrand",
    "is.unsorted",
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    "isSmallGenome",
    "makeGPosFromDataFrame",
    "makeGRangesFromDataFrame",
    "makeGRangesListFromDataFrame",
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    "nearest",
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    "score",
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    "seqinfo<-",
    "seqnames",
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    "shift",
    "show",
    "slidingWindows",
    "sort",
    "sort.GenomicRanges",
    "sort.GRangesList",
    "split",
    "start",
    "start<-",
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    "summary",
    "summary.GenomicRanges",
    "summary.GPos",
    "terminators",
    "tile",
    "tileGenome",
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    "union",
    "update",
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    "values",
    "values<-",
    "width",
    "width<-",
    "windows"
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    {
      "page": "absoluteRanges",
      "title": "Transform genomic ranges into \"absolute\" ranges",
      "topics": [
        "absoluteRanges",
        "isSmallGenome",
        "relativeRanges"
      ]
    },
    {
      "page": "constraint",
      "title": "Enforcing constraints thru Constraint objects",
      "topics": [
        "checkConstraint",
        "class:Constraint",
        "class:Constraint_OR_NULL",
        "Constraint",
        "constraint",
        "Constraint-class",
        "constraint<-",
        "Constraints",
        "Constraint_OR_NULL",
        "Constraint_OR_NULL-class"
      ]
    },
    {
      "page": "coverage-methods",
      "title": "Coverage of a GRanges or GRangesList object",
      "topics": [
        "coverage",
        "coverage,GenomicRanges-method",
        "coverage,GRangesList-method",
        "coverage,StitchedGPos-method",
        "coverage-methods"
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    },
    {
      "page": "DelegatingGenomicRanges-class",
      "title": "DelegatingGenomicRanges objects",
      "topics": [
        "class:DelegatingGenomicRanges",
        "DelegatingGenomicRanges-class",
        "ranges,DelegatingGenomicRanges-method",
        "seqinfo,DelegatingGenomicRanges-method",
        "seqnames,DelegatingGenomicRanges-method",
        "strand,DelegatingGenomicRanges-method",
        "update,DelegatingGenomicRanges-method"
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    },
    {
      "page": "findOverlaps-methods",
      "title": "Finding overlapping genomic ranges",
      "topics": [
        "countOverlaps",
        "countOverlaps,GenomicRanges,GenomicRanges-method",
        "findOverlaps",
        "findOverlaps,GenomicRanges,GenomicRanges-method",
        "findOverlaps,GenomicRanges,GRangesList-method",
        "findOverlaps,GRangesList,GenomicRanges-method",
        "findOverlaps,GRangesList,GRangesList-method",
        "findOverlaps-methods",
        "overlapsAny",
        "subsetByOverlaps"
      ]
    },
    {
      "page": "genomic-range-squeezers",
      "title": "Squeeze the genomic ranges out of a range-based object",
      "topics": [
        "genomic-range-squeezers",
        "granges",
        "grglist",
        "grglist,Pairs-method"
      ]
    },
    {
      "page": "GenomicRanges-comparison",
      "title": "Comparing and ordering genomic ranges",
      "topics": [
        "duplicated,GenomicRanges-method",
        "duplicated.GenomicRanges",
        "GenomicRanges-comparison",
        "is.unsorted,GenomicRanges-method",
        "match,GenomicRanges,GenomicRanges-method",
        "order,GenomicRanges-method",
        "pcompare",
        "pcompare,GenomicRanges,GenomicRanges-method",
        "rank,GenomicRanges-method",
        "selfmatch,GenomicRanges-method",
        "sort,GenomicRanges-method",
        "sort.GenomicRanges"
      ]
    },
    {
      "page": "GenomicRangesList-class",
      "title": "GenomicRangesList objects",
      "topics": [
        "class:CompressedGenomicRangesList",
        "class:GenomicRangesList",
        "class:GenomicRanges_OR_GenomicRangesList",
        "class:SimpleGenomicRangesList",
        "CompressedGenomicRangesList",
        "CompressedGenomicRangesList-class",
        "elementMetadata,GenomicRangesList-method",
        "elementMetadata<-,CompressedGenomicRangesList-method",
        "end<-,CompressedGenomicRangesList-method",
        "extractROWS,GenomicRangesList,ANY-method",
        "GenomicRangesList",
        "GenomicRangesList-class",
        "GenomicRanges_OR_GenomicRangesList",
        "GenomicRanges_OR_GenomicRangesList-class",
        "getListElement,GenomicRangesList-method",
        "length,GenomicRangesList-method",
        "names,GenomicRangesList-method",
        "names<-,GenomicRangesList-method",
        "score,GenomicRangesList-method",
        "score<-,GenomicRangesList-method",
        "seqinfo,CompressedGenomicRangesList-method",
        "seqinfo,GenomicRangesList-method",
        "seqinfo<-,CompressedGenomicRangesList-method",
        "seqnames,GenomicRangesList-method",
        "seqnames<-,CompressedGenomicRangesList-method",
        "show,GenomicRangesList-method",
        "SimpleGenomicRangesList",
        "SimpleGenomicRangesList-class",
        "start<-,CompressedGenomicRangesList-method",
        "strand,GenomicRangesList-method",
        "strand<-,CompressedGenomicRangesList,ANY-method",
        "strand<-,CompressedGenomicRangesList,character-method",
        "unlist,GenomicRangesList-method",
        "updateObject,GenomicRangesList-method",
        "width<-,CompressedGenomicRangesList-method"
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    },
    {
      "page": "genomicvars",
      "title": "Manipulating genomic variables",
      "topics": [
        "bindAsGRanges",
        "binnedAverage",
        "coerce,RleList,GRanges-method",
        "coerce,RleViewsList,GRanges-method",
        "genomicvariables",
        "genomicvars",
        "mcolAsRleList"
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    },
    {
      "page": "GNCList-class",
      "title": "GNCList objects",
      "topics": [
        "class:GNCList",
        "coerce,GenomicRanges,GNCList-method",
        "coerce,GNCList,GRanges-method",
        "end,GNCList-method",
        "GNCList",
        "GNCList-class",
        "granges,GNCList-method",
        "length,GNCList-method",
        "names,GNCList-method",
        "ranges,GNCList-method",
        "seqinfo,GNCList-method",
        "seqnames,GNCList-method",
        "start,GNCList-method",
        "strand,GNCList-method",
        "width,GNCList-method"
      ]
    },
    {
      "page": "GPos-class",
      "title": "Memory-efficient representation of genomic positions",
      "topics": [
        "as.data.frame,GPos-method",
        "as.data.frame.GPos",
        "class:GPos",
        "class:StitchedGPos",
        "class:UnstitchedGPos",
        "coerce,ANY,GPos-method",
        "coerce,ANY,StitchedGPos-method",
        "coerce,ANY,UnstitchedGPos-method",
        "coerce,GRanges,GPos-method",
        "coerce,GRanges,StitchedGPos-method",
        "coerce,GRanges,UnstitchedGPos-method",
        "coerce,StitchedGPos,GRanges-method",
        "coerce,UnstitchedGPos,GRanges-method",
        "from_GPos_to_GRanges",
        "GPos",
        "GPos-class",
        "pos,GPos-method",
        "show,GPos-method",
        "StitchedGPos",
        "StitchedGPos-class",
        "summary,GPos-method",
        "summary.GPos",
        "UnstitchedGPos",
        "UnstitchedGPos-class",
        "updateObject,GPos-method"
      ]
    },
    {
      "page": "GRanges-class",
      "title": "GRanges objects",
      "topics": [
        "$,GenomicRanges-method",
        "$<-,GenomicRanges-method",
        "as.character,GenomicRanges-method",
        "as.data.frame,GenomicRanges-method",
        "as.factor,GenomicRanges-method",
        "bindROWS,GenomicRanges-method",
        "class:GenomicPos",
        "class:GenomicRanges",
        "class:GRanges",
        "class:IRanges_OR_IPos",
        "coerce,ANY,GenomicRanges-method",
        "coerce,character,GRanges-method",
        "coerce,factor,GRanges-method",
        "coerce,GenomicRanges,CompressedIRangesList-method",
        "coerce,GenomicRanges,GRanges-method",
        "coerce,GenomicRanges,Grouping-method",
        "coerce,GenomicRanges,IntegerRangesList-method",
        "coerce,GenomicRanges,IRangesList-method",
        "coerce,IntegerRangesList,GRanges-method",
        "coerce,Seqinfo,GRanges-method",
        "coerce,Seqinfo,IntegerRangesList-method",
        "end<-,GenomicRanges-method",
        "GenomicPos",
        "GenomicPos-class",
        "GenomicRanges",
        "GenomicRanges-class",
        "GenomicRanges_OR_missing-class",
        "getListElement,GenomicRanges-method",
        "GRanges",
        "granges,GenomicRanges-method",
        "GRanges-class",
        "IRanges_OR_IPos",
        "IRanges_OR_IPos-class",
        "length,GenomicRanges-method",
        "names,GenomicRanges-method",
        "names<-,GenomicRanges-method",
        "parallel_slot_names,GRanges-method",
        "ranges,GRanges-method",
        "ranges<-,GenomicRanges-method",
        "score,GenomicRanges-method",
        "score<-,GenomicRanges-method",
        "seqinfo,GRanges-method",
        "seqinfo,List-method",
        "seqinfo<-,GenomicRanges-method",
        "seqinfo<-,List-method",
        "seqnames,GRanges-method",
        "seqnames<-,GenomicRanges-method",
        "show,GenomicRanges-method",
        "start,GenomicRanges-method",
        "start<-,GenomicRanges-method",
        "strand,GRanges-method",
        "strand<-,GenomicRanges,ANY-method",
        "summary,GenomicRanges-method",
        "summary.GenomicRanges",
        "update,GRanges-method",
        "updateObject,GRanges-method",
        "width,GenomicRanges-method",
        "width<-,GenomicRanges-method",
        "[,list_OR_List,GenomicRanges-method"
      ]
    },
    {
      "page": "GRangesFactor-class",
      "title": "GRangesFactor objects",
      "topics": [
        "class:GRangesFactor",
        "coerce,ANY,GRangesFactor-method",
        "coerce,Factor,GRanges-method",
        "end,GRangesFactor-method",
        "FactorToClass,GRanges-method",
        "granges,GRangesFactor-method",
        "GRangesFactor",
        "GRangesFactor-class",
        "pos,GRangesFactor-method",
        "ranges,GRangesFactor-method",
        "seqinfo,GRangesFactor-method",
        "seqnames,GRangesFactor-method",
        "show,GRangesFactor-method",
        "start,GRangesFactor-method",
        "strand,GRangesFactor-method",
        "width,GRangesFactor-method"
      ]
    },
    {
      "page": "GRangesList-class",
      "title": "GRangesList objects",
      "topics": [
        "class:CompressedGRangesList",
        "class:GenomicRanges_OR_GRangesList",
        "class:GRangesList",
        "class:SimpleGRangesList",
        "coerce,CompressedGRangesList,CompressedIRangesList-method",
        "coerce,CompressedGRangesList,IntegerRangesList-method",
        "coerce,CompressedGRangesList,IRangesList-method",
        "coerce,GenomicRangesList,SimpleGRangesList-method",
        "coerce,List,CompressedGRangesList-method",
        "coerce,list,CompressedGRangesList-method",
        "coerce,List,GRangesList-method",
        "coerce,list,GRangesList-method",
        "coerce,List,SimpleGRangesList-method",
        "coerce,list,SimpleGRangesList-method",
        "coerce,SimpleGenomicRangesList,SimpleGRangesList-method",
        "coerce,SimpleList,SimpleGRangesList-method",
        "CompressedGRangesList",
        "CompressedGRangesList-class",
        "GenomicRanges_OR_GRangesList",
        "GenomicRanges_OR_GRangesList-class",
        "GRangesList",
        "GRangesList-class",
        "makeGRangesListFromFeatureFragments",
        "ranges,CompressedGRangesList-method",
        "ranges<-,CompressedGRangesList-method",
        "relistToClass,GRanges-method",
        "SimpleGRangesList",
        "SimpleGRangesList-class",
        "sort,CompressedGRangesList-method",
        "sort,GRangesList-method",
        "sort.GRangesList",
        "[,CompressedGRangesList,ANY-method",
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        "[<-,CompressedGRangesList,ANY-method",
        "[<-,CompressedGRangesList-method"
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    },
    {
      "page": "inter-range-methods",
      "title": "Inter range transformations of a GRanges or GRangesList object",
      "topics": [
        "disjoin",
        "disjoin,GenomicRanges-method",
        "disjoin,GRangesList-method",
        "disjointBins",
        "disjointBins,GenomicRanges-method",
        "gaps",
        "gaps,GenomicRanges-method",
        "inter-range-methods",
        "isDisjoint",
        "isDisjoint,GenomicRanges-method",
        "isDisjoint,GRangesList-method",
        "isDisjoint,StitchedGPos-method",
        "range",
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        "range,GRangesList-method",
        "range,StitchedGPos-method",
        "reduce",
        "reduce,GenomicRanges-method",
        "reduce,GRangesList-method"
      ]
    },
    {
      "page": "intra-range-methods",
      "title": "Intra range transformations of a GRanges or GRangesList object",
      "topics": [
        "flank",
        "flank,GenomicRanges-method",
        "intra-range-methods",
        "narrow",
        "narrow,GenomicRanges-method",
        "promoters",
        "promoters,GenomicRanges-method",
        "resize",
        "resize,GenomicRanges-method",
        "restrict",
        "restrict,GenomicRanges-method",
        "shift",
        "shift,GenomicRanges-method",
        "terminators",
        "terminators,GenomicRanges-method",
        "trim",
        "trim,GenomicRanges-method",
        "trim,GRangesList-method",
        "update_ranges,GenomicRanges-method"
      ]
    },
    {
      "page": "makeGRangesFromDataFrame",
      "title": "Make a GRanges object from a data.frame or DataFrame",
      "topics": [
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        "coerce,data.frame,GRanges-method",
        "coerce,DataFrame,GPos-method",
        "coerce,DataFrame,GRanges-method",
        "makeGPosFromDataFrame",
        "makeGRangesFromDataFrame"
      ]
    },
    {
      "page": "makeGRangesListFromDataFrame",
      "title": "Make a GRangesList object from a data.frame or DataFrame",
      "topics": [
        "makeGRangesListFromDataFrame"
      ]
    },
    {
      "page": "nearest-methods",
      "title": "Finding the nearest genomic range/position neighbor",
      "topics": [
        "distance",
        "distance,GenomicRanges,GenomicRanges-method",
        "distanceToNearest",
        "distanceToNearest,GenomicRanges,GenomicRanges-method",
        "distanceToNearest,GenomicRanges,missing-method",
        "follow",
        "follow,GenomicRanges,GenomicRanges-method",
        "follow,GenomicRanges,missing-method",
        "nearest",
        "nearest,GenomicRanges,GenomicRanges-method",
        "nearest,GenomicRanges,missing-method",
        "nearest-methods",
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        "nearestKNeighbors,GenomicRanges,missing-method",
        "precede",
        "precede,GenomicRanges,GenomicRanges-method",
        "precede,GenomicRanges,missing-method"
      ]
    },
    {
      "page": "phicoef",
      "title": "Calculate the \"phi coefficient\" between two binary variables",
      "topics": [
        "phicoef"
      ]
    },
    {
      "page": "setops-methods",
      "title": "Set operations on genomic ranges",
      "topics": [
        "intersect",
        "intersect,GenomicRanges,GenomicRanges-method",
        "intersect,GenomicRanges,Vector-method",
        "intersect,GRangesList,GRangesList-method",
        "intersect,Vector,GenomicRanges-method",
        "pgap",
        "pgap,GRanges,GRanges-method",
        "pintersect",
        "pintersect,GRanges,GRanges-method",
        "pintersect,GRanges,GRangesList-method",
        "pintersect,GRangesList,GRanges-method",
        "psetdiff",
        "psetdiff,GRanges,GRanges-method",
        "psetdiff,GRanges,GRangesList-method",
        "punion",
        "punion,GRanges,GRanges-method",
        "punion,GRanges,GRangesList-method",
        "punion,GRangesList,GRanges-method",
        "setdiff",
        "setdiff,GenomicRanges,GenomicRanges-method",
        "setdiff,GenomicRanges,Vector-method",
        "setdiff,GRangesList,GRangesList-method",
        "setdiff,Vector,GenomicRanges-method",
        "setops-methods",
        "union",
        "union,GenomicRanges,GenomicRanges-method",
        "union,GenomicRanges,Vector-method",
        "union,GRangesList,GRangesList-method",
        "union,Vector,GenomicRanges-method"
      ]
    },
    {
      "page": "strand-utils",
      "title": "Strand utilities",
      "topics": [
        "invertStrand,character-method",
        "invertStrand,factor-method",
        "invertStrand,integer-method",
        "invertStrand,logical-method",
        "invertStrand,NULL-method",
        "invertStrand,Rle-method",
        "invertStrand,RleList-method",
        "strand,character-method",
        "strand,DataFrame-method",
        "strand,factor-method",
        "strand,integer-method",
        "strand,logical-method",
        "strand,missing-method",
        "strand,NULL-method",
        "strand,Rle-method",
        "strand,RleList-method",
        "strand-utils",
        "strand<-,DataFrame,ANY-method"
      ]
    },
    {
      "page": "subtract-methods",
      "title": "Subtract a set of genomic ranges from a GRanges object",
      "topics": [
        "subtract",
        "subtract,GenomicRanges,GenomicRanges-method",
        "subtract-methods"
      ]
    },
    {
      "page": "tile-methods",
      "title": "Generate windows for a GenomicRanges",
      "topics": [
        "slidingWindows",
        "slidingWindows,GenomicRanges-method",
        "tile",
        "tile,GenomicRanges-method",
        "tile-methods"
      ]
    },
    {
      "page": "tileGenome",
      "title": "Put (virtual) tiles on a given genome",
      "topics": [
        "tileGenome"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GenomicRanges/raw/HEAD/README.md",
  "_rundeps": [
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      "source": "GenomicRangesIntroduction.Rmd",
      "filename": "GenomicRangesIntroduction.html",
      "title": "An Introduction to the GenomicRanges Package",
      "author": "Marc Carlson, Patrick Aboyoun, Hervé Pagès, and Martin Morgan",
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      "headings": [
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        "GRanges: Genomic Ranges",
        "Splitting and combining GRanges objects",
        "Subsetting  GRanges objects",
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        "Interval set operations for GRanges objects",
        "GRangesList: Groups of Genomic Ranges",
        "Basic GRangesList accessors",
        "Combining GRangesList objects",
        "Basic interval operations for GRangesList objects",
        "Subsetting GRangesList objects",
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      "source": "GRanges_and_GRangesList_slides.Rnw",
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      "created": "2015-02-04 09:48:40",
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      "source": "Ten_things_slides.Rnw",
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      "headings": [],
      "created": "2016-06-25 04:54:11",
      "modified": "2022-12-07 14:22:45",
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      "source": "ExtendingGenomicRanges.Rnw",
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      "title": "Extending GenomicRanges ",
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      "created": "2014-10-03 22:06:34",
      "modified": "2016-12-13 22:41:43",
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