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  "Title": "A container (S4 class) for matrix-like assays",
  "Description": "The SummarizedExperiment container contains one or more\nassays, each represented by a matrix-like object of numeric or\nother mode. The rows typically represent genomic ranges of\ninterest and the columns represent samples.",
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  "Authors@R": "c(\nperson(\"Martin\", \"Morgan\", role=\"aut\"),\nperson(\"Valerie\", \"Obenchain\", role=\"aut\"),\nperson(\"Jim\", \"Hester\", role=\"aut\"),\nperson(\"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 12:41:19 UTC",
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  "_exports": [
    ".DollarNames.RangedSummarizedExperiment",
    ".DollarNames.SummarizedExperiment",
    "acbind",
    "arbind",
    "as.data.frame",
    "assay",
    "assay<-",
    "assayNames",
    "assayNames<-",
    "assays",
    "Assays",
    "assays<-",
    "cbind",
    "coerce",
    "colData",
    "colData<-",
    "colnames",
    "combineCols",
    "combineRows",
    "Compare",
    "coverage",
    "disjointBins",
    "distance",
    "distanceToNearest",
    "duplicated",
    "elementMetadata",
    "elementMetadata<-",
    "end",
    "end<-",
    "findOverlaps",
    "flank",
    "follow",
    "geneRangeMapper",
    "horizontal_slot_names",
    "is.unsorted",
    "isDisjoint",
    "makeSummarizedExperimentFromDataFrame",
    "makeSummarizedExperimentFromExpressionSet",
    "makeSummarizedExperimentFromLoom",
    "match",
    "mcols",
    "mcols<-",
    "merge",
    "metadata<-",
    "naiveRangeMapper",
    "narrow",
    "ncol",
    "nearest",
    "nrow",
    "order",
    "parallel_slot_names",
    "pcompare",
    "precede",
    "probeRangeMapper",
    "promoters",
    "ranges",
    "ranges<-",
    "rank",
    "rbind",
    "realize",
    "resize",
    "restrict",
    "rowData",
    "rowData<-",
    "rownames",
    "rowRanges",
    "rowRanges<-",
    "saveRDS",
    "seqinfo",
    "seqinfo<-",
    "seqnames",
    "seqnames<-",
    "shift",
    "show",
    "showAsCell",
    "sort",
    "start",
    "start<-",
    "strand",
    "strand<-",
    "subset",
    "SummarizedExperiment",
    "terminators",
    "trim",
    "updateObject",
    "values",
    "values<-",
    "vertical_slot_names",
    "width",
    "width<-"
  ],
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    {
      "page": "Assays-class",
      "title": "Assays objects",
      "topics": [
        "acbind,Matrix-method",
        "arbind,Matrix-method",
        "Assays",
        "Assays-class",
        "AssaysInEnv",
        "AssaysInEnv-class",
        "cbind,Assays-method",
        "class:Assays",
        "class:AssaysInEnv",
        "class:ShallowData",
        "class:ShallowSimpleListAssays",
        "class:SimpleAssays",
        "coerce,AssaysInEnv,SimpleList-method",
        "coerce,ShallowSimpleListAssays,SimpleList-method",
        "coerce,SimpleAssays,SimpleList-method",
        "coerce,SimpleList,AssaysInEnv-method",
        "coerce,SimpleList,ShallowSimpleListAssays-method",
        "coerce,SimpleList,SimpleAssays-method",
        "dim,Assays-method",
        "getListElement,Assays-method",
        "getListElement,AssaysInEnv-method",
        "length,Assays-method",
        "length,AssaysInEnv-method",
        "names,Assays-method",
        "names,AssaysInEnv-method",
        "names<-,Assays-method",
        "names<-,AssaysInEnv-method",
        "rbind,Assays-method",
        "setListElement,Assays-method",
        "setListElement,AssaysInEnv-method",
        "ShallowData",
        "ShallowData-class",
        "ShallowSimpleListAssays",
        "ShallowSimpleListAssays-class",
        "SimpleAssays",
        "SimpleAssays-class",
        "updateObject,Assays-method",
        "[,Assays,ANY,ANY,ANY-method",
        "[,Assays,ANY-method",
        "[<-,Assays,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "coverage-methods",
      "title": "Coverage of a RangedSummarizedExperiment object",
      "topics": [
        "coverage",
        "coverage,RangedSummarizedExperiment-method",
        "coverage-methods"
      ]
    },
    {
      "page": "findOverlaps-methods",
      "title": "Finding overlapping ranges in RangedSummarizedExperiment objects",
      "topics": [
        "findOverlaps",
        "findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "findOverlaps,RangedSummarizedExperiment,Vector-method",
        "findOverlaps,Vector,RangedSummarizedExperiment-method",
        "findOverlaps-methods"
      ]
    },
    {
      "page": "inter-range-methods",
      "title": "Inter range transformations of a RangedSummarizedExperiment object",
      "topics": [
        "disjointBins",
        "disjointBins,RangedSummarizedExperiment-method",
        "inter-range-methods",
        "isDisjoint",
        "isDisjoint,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "intra-range-methods",
      "title": "Intra range transformations of a RangedSummarizedExperiment object",
      "topics": [
        "flank",
        "flank,RangedSummarizedExperiment-method",
        "intra-range-methods",
        "narrow",
        "narrow,RangedSummarizedExperiment-method",
        "promoters",
        "promoters,RangedSummarizedExperiment-method",
        "resize",
        "resize,RangedSummarizedExperiment-method",
        "restrict",
        "restrict,RangedSummarizedExperiment-method",
        "shift",
        "shift,RangedSummarizedExperiment-method",
        "terminators",
        "terminators,RangedSummarizedExperiment-method",
        "trim,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "makeSummarizedExperimentFromDataFrame",
      "title": "Make a RangedSummarizedExperiment from a data.frame or DataFrame",
      "topics": [
        "makeSummarizedExperimentFromDataFrame"
      ]
    },
    {
      "page": "makeSummarizedExperimentFromExpressionSet",
      "title": "Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa",
      "topics": [
        "coerce,ExpressionSet,RangedSummarizedExperiment-method",
        "coerce,ExpressionSet,SummarizedExperiment-method",
        "coerce,RangedSummarizedExperiment,ExpressionSet-method",
        "coerce,SummarizedExperiment,ExpressionSet-method",
        "geneRangeMapper",
        "makeSummarizedExperimentFromExpressionSet",
        "naiveRangeMapper",
        "probeRangeMapper"
      ]
    },
    {
      "page": "makeSummarizedExperimentFromLoom",
      "title": "Make a SummarizedExperiment from a '.loom' hdf5 file",
      "topics": [
        "makeSummarizedExperimentFromLoom"
      ]
    },
    {
      "page": "nearest-methods",
      "title": "Finding the nearest range neighbor in RangedSummarizedExperiment objects",
      "topics": [
        "distance",
        "distance,ANY,RangedSummarizedExperiment-method",
        "distance,RangedSummarizedExperiment,ANY-method",
        "distance,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "distanceToNearest",
        "distanceToNearest,ANY,RangedSummarizedExperiment-method",
        "distanceToNearest,RangedSummarizedExperiment,ANY-method",
        "distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "follow",
        "follow,ANY,RangedSummarizedExperiment-method",
        "follow,RangedSummarizedExperiment,ANY-method",
        "follow,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "nearest",
        "nearest,ANY,RangedSummarizedExperiment-method",
        "nearest,RangedSummarizedExperiment,ANY-method",
        "nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "nearest-methods",
        "precede",
        "precede,ANY,RangedSummarizedExperiment-method",
        "precede,RangedSummarizedExperiment,ANY-method",
        "precede,RangedSummarizedExperiment,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "RangedSummarizedExperiment-class",
      "title": "RangedSummarizedExperiment objects",
      "topics": [
        "class:RangedSummarizedExperiment",
        "coerce,RangedSummarizedExperiment,SummarizedExperiment-method",
        "coerce,SummarizedExperiment,RangedSummarizedExperiment-method",
        "Compare,ANY,RangedSummarizedExperiment-method",
        "Compare,RangedSummarizedExperiment,ANY-method",
        "Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "dimnames<-,RangedSummarizedExperiment,list-method",
        "duplicated,RangedSummarizedExperiment-method",
        "elementMetadata,RangedSummarizedExperiment-method",
        "elementMetadata<-,RangedSummarizedExperiment-method",
        "end,RangedSummarizedExperiment-method",
        "end<-,RangedSummarizedExperiment-method",
        "granges,RangedSummarizedExperiment-method",
        "is.unsorted,RangedSummarizedExperiment-method",
        "mcols,RangedSummarizedExperiment-method",
        "mcols<-,RangedSummarizedExperiment-method",
        "names,RangedSummarizedExperiment-method",
        "names<-,RangedSummarizedExperiment-method",
        "order,RangedSummarizedExperiment-method",
        "parallel_slot_names,RangedSummarizedExperiment-method",
        "pcompare,ANY,RangedSummarizedExperiment-method",
        "pcompare,RangedSummarizedExperiment,ANY-method",
        "pcompare,RangedSummarizedExperiment,RangedSummarizedExperiment-method",
        "RangedSummarizedExperiment",
        "RangedSummarizedExperiment-class",
        "ranges,RangedSummarizedExperiment-method",
        "ranges<-,RangedSummarizedExperiment-method",
        "rank,RangedSummarizedExperiment-method",
        "rowRanges",
        "rowRanges,RangedSummarizedExperiment-method",
        "rowRanges,SummarizedExperiment-method",
        "rowRanges<-",
        "rowRanges<-,RangedSummarizedExperiment,NULL-method",
        "rowRanges<-,SummarizedExperiment,GenomicRanges-method",
        "rowRanges<-,SummarizedExperiment,GRangesList-method",
        "rowRanges<-,SummarizedExperiment,NULL-method",
        "seqinfo,RangedSummarizedExperiment-method",
        "seqinfo<-,RangedSummarizedExperiment-method",
        "seqnames,RangedSummarizedExperiment-method",
        "sort,RangedSummarizedExperiment-method",
        "split,RangedSummarizedExperiment,ANY-method",
        "split,RangedSummarizedExperiment-method",
        "start,RangedSummarizedExperiment-method",
        "start<-,RangedSummarizedExperiment-method",
        "strand,RangedSummarizedExperiment-method",
        "strand<-,RangedSummarizedExperiment,ANY-method",
        "subset,RangedSummarizedExperiment-method",
        "updateObject,RangedSummarizedExperiment-method",
        "width,RangedSummarizedExperiment-method",
        "width<-,RangedSummarizedExperiment-method"
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    },
    {
      "page": "SummarizedExperiment-class",
      "title": "SummarizedExperiment objects",
      "topics": [
        "$,SummarizedExperiment-method",
        "$<-,SummarizedExperiment-method",
        "assay",
        "assay,SummarizedExperiment,character-method",
        "assay,SummarizedExperiment,missing-method",
        "assay,SummarizedExperiment,numeric-method",
        "assay<-",
        "assay<-,SummarizedExperiment,character-method",
        "assay<-,SummarizedExperiment,missing-method",
        "assay<-,SummarizedExperiment,numeric-method",
        "assayNames",
        "assayNames,SummarizedExperiment-method",
        "assayNames<-",
        "assayNames<-,SummarizedExperiment,character-method",
        "assays",
        "assays,SummarizedExperiment-method",
        "assays<-",
        "assays<-,SummarizedExperiment,list-method",
        "assays<-,SummarizedExperiment,SimpleList-method",
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