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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": "1.64.0",
  "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-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:30 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicRanges",
  "RemoteRef": "RELEASE_3_23",
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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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    "makeGPosFromDataFrame",
    "makeGRangesFromDataFrame",
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    "sort",
    "sort.GenomicRanges",
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    "split",
    "start",
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    "tile",
    "tileGenome",
    "trim",
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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"
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    {
      "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": [
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        "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"
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    },
    {
      "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"
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    },
    {
      "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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    {
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      "title": "Manipulating genomic variables",
      "topics": [
        "bindAsGRanges",
        "binnedAverage",
        "coerce,RleList,GRanges-method",
        "coerce,RleViewsList,GRanges-method",
        "genomicvariables",
        "genomicvars",
        "mcolAsRleList"
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    },
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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",
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    {
      "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",
        "[<-,CompressedGRangesList,ANY,ANY,ANY-method",
        "[<-,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",
        "range,GenomicRanges-method",
        "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"
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    },
    {
      "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",
        "nearestKNeighbors",
        "nearestKNeighbors,GenomicRanges,GenomicRanges-method",
        "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",
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        "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"
      ]
    }
  ],
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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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        "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",
        "Looping over GRangesList objects",
        "Interval overlaps involving GRanges and GRangesList objects",
        "Finding the nearest genomic position in GRanges objects",
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      "created": "2018-07-30 19:53:25",
      "modified": "2024-06-10 22:26:37",
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      "source": "GenomicRangesHOWTOs.Rnw",
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      "source": "GRanges_and_GRangesList_slides.Rnw",
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      "engine": "utils::Sweave",
      "headings": [
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      "created": "2015-02-04 09:48:40",
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      "source": "Ten_things_slides.Rnw",
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      "title": "Ten Things You Didn't Know (slides from BioC 2016) ",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2016-06-25 04:54:11",
      "modified": "2022-12-07 14:22:45",
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    {
      "source": "ExtendingGenomicRanges.Rnw",
      "filename": "ExtendingGenomicRanges.pdf",
      "title": "Extending GenomicRanges ",
      "engine": "utils::Sweave",
      "headings": [
        "1 Introduction",
        "2 The GenomicRanges abstraction",
        "3 Formalizing mcols: Extra column slots"
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      "created": "2014-10-03 22:06:34",
      "modified": "2016-12-13 22:41:43",
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