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  "Package": "MultiAssayExperiment",
  "Title": "Software for the integration of multi-omics experiments in\nBioconductor",
  "Version": "1.39.0",
  "Authors@R": "c(\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\",\nc(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3242-0582\")),\nperson(\"Martin\", \"Morgan\", , , c(\"aut\", \"ctb\")),\nperson(\"Lori\", \"Shepherd\", , , \"ctb\"),\nperson(\"Hervé\", \"Pagès\", , , \"ctb\"),\nperson(\"Vincent J\", \"Carey\", , , c(\"aut\", \"ctb\")),\nperson(\"Levi\", \"Waldron\", , \"lwaldron.research@gmail.com\", \"aut\"),\nperson(\"MultiAssay\", \"SIG\", , \"biocmultiassay@googlegroups.com\", \"ctb\"),\nperson(\"NCI\", role = \"fnd\", comment = c(GrantNo. = \"U24CA289073\"))\n)",
  "Description": "Harmonize data management of multiple experimental assays\nperformed on an overlapping set of specimens.  It provides a\nfamiliar Bioconductor user experience by extending concepts\nfrom SummarizedExperiment, supporting an open-ended mix of\nstandard data classes for individual assays, and allowing\nsubsetting by genomic ranges or rownames. Facilities are\nprovided for reshaping data into wide and long formats for\nadaptability to graphing and downstream analysis.",
  "License": "Artistic-2.0",
  "URL": "http://waldronlab.io/MultiAssayExperiment/",
  "BugReports": "https://github.com/waldronlab/MultiAssayExperiment/issues",
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  "Collate": "'ExperimentList-class.R' 'MultiAssayExperiment-class.R'\n'MatchedAssayExperiment-class.R' 'subsetBy-methods.R'\n'MultiAssayExperiment-subset.R'\n'MultiAssayExperiment-methods.R'\n'MultiAssayExperiment-helpers.R' 'MultiAssayExperiment-pkg.R'\n'MultiAssayExperimentToMAF.R' 'assay-methods.R' 'data.R'\n'hasAssay.R' 'listToMap.R' 'mapToList.R' 'prepMultiAssay.R'\n'reexports.R' 'saveHDF5MultiAssayExperiment.R' 'upsetSamples.R'\n'utilities.R'",
  "Date": "2026-03-28",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:09 UTC",
  "RemoteUrl": "https://github.com/bioc/MultiAssayExperiment",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Marcel Ramos [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3242-0582>),\nMartin Morgan [aut, ctb],\nLori Shepherd [ctb],\nHervé Pagès [ctb],\nVincent J Carey [aut, ctb],\nLevi Waldron [aut],\nMultiAssay SIG [ctb],\nNCI [fnd] (GrantNo.: U24CA289073)",
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    "assay",
    "assays",
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    "hasAssay",
    "hasRowData",
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    "intersectByRowData",
    "intersectColumns",
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    "isEmpty",
    "listToMap",
    "loadHDF5MultiAssayExperiment",
    "longForm",
    "makeHitList",
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    "MatchedAssayExperiment",
    "mergeReplicates",
    "metadata",
    "metadata<-",
    "MultiAssayExperiment",
    "MultiAssayExperimentToMAF",
    "prepMultiAssay",
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    "saveHDF5MultiAssayExperiment",
    "show",
    "showReplicated",
    "splitAssays",
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    "subsetByColData",
    "subsetByColumn",
    "subsetByRow",
    "subsetByRowData",
    "updateObject",
    "upsetSamples",
    "wideFormat"
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      "object": "miniACC",
      "file": "miniACC.RData",
      "class": [
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      "table": false,
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      "page": "MultiAssayExperiment-package",
      "title": "MultiAssayExperiment: Build an integrative multi-assay container",
      "topics": [
        "MultiAssayExperiment-package"
      ]
    },
    {
      "page": "ExperimentList",
      "title": "Represent multiple experiments as a List-derivative 'ExperimentList'",
      "topics": [
        "ExperimentList"
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    {
      "page": "ExperimentList-class",
      "title": "ExperimentList - A container for multi-experiment data",
      "topics": [
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        "assay,ExperimentList,character-method",
        "assay,ExperimentList,missing-method",
        "assay,ExperimentList,numeric-method",
        "assays,ExperimentList-method",
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        "rownames,ExperimentList-method",
        "show,ExperimentList-method"
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    },
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      "title": "Checking assay method for any class",
      "topics": [
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        "loadHDF5MultiAssayExperiment",
        "saveHDF5MultiAssayExperiment"
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      "title": "MatchedAssayExperiment - A matched-samples MultiAssayExperiment class",
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        "MatchedAssayExperiment",
        "MatchedAssayExperiment-class"
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    {
      "page": "miniACC",
      "title": "Adrenocortical Carcinoma (ACC) MultiAssayExperiment",
      "topics": [
        "miniACC"
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    },
    {
      "page": "MultiAssayExperiment",
      "title": "Construct an integrative representation of multi-omic data with 'MultiAssayExperiment'",
      "topics": [
        "MultiAssayExperiment"
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      "page": "MultiAssayExperiment-class",
      "title": "MultiAssayExperiment - An integrative multi-assay class for experiment data",
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        "assay,MultiAssayExperiment,missing-method",
        "assay,MultiAssayExperiment,numeric-method",
        "assays,MultiAssayExperiment-method",
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        "show,MultiAssayExperiment-method",
        "updateObject,MultiAssayExperiment-method"
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    },
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      "page": "MultiAssayExperiment-helpers",
      "title": "A group of helper functions for manipulating and cleaning a MultiAssayExperiment",
      "topics": [
        "anyReplicated",
        "anyReplicated,MultiAssayExperiment-method",
        "complete.cases,MultiAssayExperiment-method",
        "getWithColData",
        "hasRowData",
        "hasRowData,ExperimentList-method",
        "hasRowData,MultiAssayExperiment-method",
        "hasRowRanges",
        "hasRowRanges,ExperimentList-method",
        "hasRowRanges,MultiAssayExperiment-method",
        "intersectColumns",
        "intersectRows",
        "isEmpty,MultiAssayExperiment-method",
        "longForm,ANY-method",
        "longForm,ExperimentList-method",
        "longForm,MultiAssayExperiment-method",
        "makeHitList",
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        "mergeReplicates",
        "mergeReplicates,ANY-method",
        "mergeReplicates,MultiAssayExperiment-method",
        "MultiAssayExperiment-helpers",
        "renameColname",
        "renamePrimary",
        "replicated",
        "replicated,MultiAssayExperiment-method",
        "replicates",
        "replicates,MultiAssayExperiment-method",
        "showReplicated",
        "showReplicated,MultiAssayExperiment-method",
        "splitAssays",
        "splitAssays,MultiAssayExperiment-method",
        "wideFormat"
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      "title": "Accessing and modifying information in MultiAssayExperiment",
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        "$,MultiAssayExperiment-method",
        "$<-,MultiAssayExperiment-method",
        "colData,MultiAssayExperiment-method",
        "colData<-,MultiAssayExperiment,ANY-method",
        "colData<-,MultiAssayExperiment,DataFrame-method",
        "colnames<-,MultiAssayExperiment,List-method",
        "colnames<-,MultiAssayExperiment,list-method",
        "drops",
        "drops,MultiAssayExperiment-method",
        "drops<-",
        "drops<-,MultiAssayExperiment-method",
        "experiments",
        "experiments,MultiAssayExperiment-method",
        "experiments<-",
        "experiments<-,MultiAssayExperiment,ExperimentList-method",
        "experiments<-,MultiAssayExperiment,List-method",
        "metadata,MultiAssayExperiment-method",
        "metadata<-,MultiAssayExperiment-method",
        "MultiAssayExperiment-methods",
        "names<-,MultiAssayExperiment-method",
        "sampleMap",
        "sampleMap,MultiAssayExperiment-method",
        "sampleMap<-",
        "sampleMap<-,MultiAssayExperiment,ANY-method",
        "sampleMap<-,MultiAssayExperiment,DataFrame-method"
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    {
      "page": "MultiAssayExperimentToMAF",
      "title": "Convert MultiAssayExperiment to MAF class",
      "topics": [
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      "page": "prepMultiAssay",
      "title": "Prepare a 'MultiAssayExperiment' instance",
      "topics": [
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      "page": "reexports",
      "title": "Objects exported from other packages",
      "topics": [
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        "reexports"
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      "page": "subsetBy",
      "title": "Subsetting a MultiAssayExperiment object",
      "topics": [
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        "intersectByRowData,MultiAssayExperiment,character,character-method",
        "subset",
        "subsetBy",
        "subsetByAssay",
        "subsetByAssay,ExperimentList-method",
        "subsetByAssay,MultiAssayExperiment-method",
        "subsetByColData",
        "subsetByColData,MultiAssayExperiment,ANY-method",
        "subsetByColData,MultiAssayExperiment,character-method",
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        "subsetByColumn,ExperimentList,List-method",
        "subsetByColumn,ExperimentList,list-method",
        "subsetByColumn,ExperimentList,logical-method",
        "subsetByColumn,MultiAssayExperiment,ANY-method",
        "subsetByRow",
        "subsetByRow,ExperimentList,ANY-method",
        "subsetByRow,ExperimentList,List-method",
        "subsetByRow,ExperimentList,list-method",
        "subsetByRow,ExperimentList,logical-method",
        "subsetByRow,MultiAssayExperiment,ANY-method",
        "subsetByRow,MultiAssayExperiment,List-method",
        "subsetByRow,MultiAssayExperiment,list-method",
        "subsetByRowData",
        "subsetByRowData,MultiAssayExperiment,character,character-method",
        "[,MultiAssayExperiment,ANY,ANY,ANY-method",
        "[,MultiAssayExperiment,ANY-method",
        "[<-,MultiAssayExperiment,ANY,ANY,ANY-method",
        "[[,MultiAssayExperiment,ANY,ANY-method",
        "[[<-,MultiAssayExperiment,ANY,ANY-method"
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