{
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  "Package": "Biobase",
  "Title": "Biobase: Base functions for Bioconductor",
  "Description": "Functions that are needed by many other packages or which\nreplace R functions.",
  "biocViews": "Infrastructure",
  "URL": "https://bioconductor.org/packages/Biobase",
  "BugReports": "https://github.com/Bioconductor/Biobase/issues",
  "Version": "2.73.1",
  "License": "Artistic-2.0",
  "Authors@R": "c(\nperson(\"R.\", \"Gentleman\", role=\"aut\"),\nperson(\"V.\", \"Carey\", role = \"aut\"),\nperson(\"M.\", \"Morgan\", role=\"aut\"),\nperson(\"S.\", \"Falcon\", role=\"aut\"),\nperson(\"Haleema\", \"Khan\",\nrole = \"ctb\",\ncomment = \"'esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML\"\n),\nperson(\"Bioconductor Package Maintainer\",\nrole = \"cre\",\nemail = \"maintainer@bioconductor.org\"\n))",
  "VignetteBuilder": "knitr",
  "LazyLoad": "yes",
  "Collate": "tools.R strings.R environment.R vignettes.R packages.R\nAllGenerics.R VersionsClass.R VersionedClasses.R\nmethods-VersionsNull.R methods-VersionedClass.R DataClasses.R\nmethods-aggregator.R methods-container.R methods-MIAxE.R\nmethods-MIAME.R methods-AssayData.R\nmethods-AnnotatedDataFrame.R methods-eSet.R\nmethods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R\nmethods-NChannelSet.R anyMissing.R rowOp-methods.R\nupdateObjectTo.R methods-ScalarObject.R zzz.R",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 23:00:16 UTC",
  "RemoteUrl": "https://github.com/bioc/Biobase",
  "RemoteRef": "HEAD",
  "RemoteSha": "c1f775a5db43b9f30fe5fb71ef2d60cc3ca851b9",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-16 09:12:59 UTC",
    "User": "root"
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  "Author": "R. Gentleman [aut],\nV. Carey [aut],\nM. Morgan [aut],\nS. Falcon [aut],\nHaleema Khan [ctb] ('esApply' and 'BiobaseDevelopment' vignette\ntranslation from Sweave to Rmarkdown / HTML),\nBioconductor Package Maintainer [cre]",
  "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
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  "_user": "bioc",
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  "_created": "2026-05-16T09:12:59.000Z",
  "_published": "2026-05-27T07:59:16.867Z",
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    "message": "Biobase 2.73.1: Get rid of stuff that has been defunct for 10+ years\n\nThis includes things like classes exprSet, phenoData, and annotatedDataset,\nor the l2e() function, etc...\n",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_mentions": 104,
  "_devurl": "https://github.com/bioconductor/biobase",
  "_searchresults": 8048,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/biobase",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "abstract",
    "addVigs2WinMenu",
    "aggenv",
    "aggfun",
    "Aggregate",
    "AnnotatedDataFrame",
    "annotatedDataFrameFrom",
    "annotation",
    "annotation<-",
    "anyMissing",
    "as.data.frame.ExpressionSet",
    "assayData",
    "assayData<-",
    "assayDataElement",
    "assayDataElement<-",
    "assayDataElementNames",
    "assayDataElementReplace",
    "assayDataNew",
    "assayDataValidMembers",
    "cache",
    "channel",
    "channelNames",
    "channelNames<-",
    "classVersion",
    "classVersion<-",
    "coerce",
    "combine",
    "Compare",
    "content",
    "contents",
    "copyEnv",
    "copySubstitute",
    "createPackage",
    "description",
    "description<-",
    "dimLabels",
    "dimLabels<-",
    "dims",
    "dumpPackTxt",
    "esApply",
    "experimentData",
    "experimentData<-",
    "expinfo",
    "ExpressionSet",
    "exprs",
    "exprs<-",
    "fData",
    "fData<-",
    "featureData",
    "featureData<-",
    "featureNames",
    "featureNames<-",
    "fvarLabels",
    "fvarLabels<-",
    "fvarMetadata",
    "fvarMetadata<-",
    "getPkgVigs",
    "hybridizations",
    "initfun",
    "initialize",
    "isCurrent",
    "isUnique",
    "isVersioned",
    "lcPrefix",
    "lcPrefixC",
    "lcSuffix",
    "listLen",
    "locked",
    "makeDataPackage",
    "matchpt",
    "MIAME",
    "mkScalar",
    "multiassign",
    "NChannelSet",
    "normControls",
    "note",
    "notes",
    "notes<-",
    "openPDF",
    "openVignette",
    "otherInfo",
    "package.version",
    "pData",
    "pData<-",
    "phenoData",
    "phenoData<-",
    "preproc",
    "preproc<-",
    "protocolData",
    "protocolData<-",
    "pubMedIds",
    "pubMedIds<-",
    "read.AnnotatedDataFrame",
    "read.MIAME",
    "readExpressionSet",
    "reverseSplit",
    "rowMax",
    "rowMedians",
    "rowMin",
    "rowQ",
    "sampleNames",
    "sampleNames<-",
    "samples",
    "se.exprs",
    "se.exprs<-",
    "selectChannels",
    "selectSome",
    "show",
    "snpCall",
    "snpCall<-",
    "snpCallProbability",
    "snpCallProbability<-",
    "storageMode",
    "storageMode<-",
    "strbreak",
    "subListExtract",
    "testBioCConnection",
    "updateObject",
    "updateObjectTo",
    "updateOldESet",
    "userQuery",
    "validMsg",
    "varLabels",
    "varLabels<-",
    "varMetadata",
    "varMetadata<-",
    "write.AnnotatedDataFrame",
    "write.exprs"
  ],
  "_datasets": [
    {
      "name": "aaMap",
      "title": "Dataset: Names and Characteristics of Amino Acids",
      "object": "aaMap",
      "file": "aaMap.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "let.1",
        "let.3",
        "scProp",
        "hyPhilic",
        "acidic"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "geneCov",
      "title": "Sample expression matrix and phenotype data.frames.",
      "object": "geneCov",
      "file": "geneCov.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cov1",
        "cov2",
        "cov3"
      ],
      "rows": 26,
      "table": true,
      "tojson": true
    },
    {
      "name": "geneCovariate",
      "title": "Sample expression matrix and phenotype data.frames.",
      "object": "geneCovariate",
      "file": "geneCovariate.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sex",
        "type",
        "score"
      ],
      "rows": 26,
      "table": true,
      "tojson": true
    },
    {
      "name": "geneData",
      "title": "Sample expression matrix and phenotype data.frames.",
      "object": "geneData",
      "file": "geneData.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E",
        "F",
        "G",
        "H",
        "I",
        "J",
        "K",
        "L",
        "M",
        "N",
        "O",
        "P",
        "Q",
        "R",
        "S",
        "T",
        "U",
        "V",
        "W",
        "X",
        "Y",
        "Z"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "reporter",
      "title": "Example data.frame representing reporter information",
      "object": "reporter",
      "file": "reporter.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "probeType"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample.ExpressionSet",
      "title": "Dataset of class 'ExpressionSet'",
      "object": "sample.ExpressionSet",
      "file": "sample.ExpressionSet.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sample.MultiSet",
      "title": "Data set of class 'MultiSet'",
      "object": "sample.MultiSet",
      "file": "sample.MultiSet.rda",
      "class": [
        "MultiSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seD",
      "title": "Sample expression matrix and phenotype data.frames.",
      "object": "seD",
      "file": "seD.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E",
        "F",
        "G",
        "H",
        "I",
        "J",
        "K",
        "L",
        "M",
        "N",
        "O",
        "P",
        "Q",
        "R",
        "S",
        "T",
        "U",
        "V",
        "W",
        "X",
        "Y",
        "Z"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "SW",
      "title": "Class to Contain High-Throughput Assays and Experimental Metadata",
      "object": "SW",
      "file": "SW.rda",
      "class": [
        "RGList"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Biobase-package",
      "title": "Biobase Package Overview",
      "topics": [
        "Biobase-package",
        "Biobase"
      ]
    },
    {
      "page": "abstract",
      "title": "Retrieve Meta-data from eSets and ExpressionSets.",
      "topics": [
        "abstract",
        "experimentData",
        "experimentData<-",
        "pubMedIds",
        "pubMedIds<-"
      ]
    },
    {
      "page": "addVig2Menu",
      "title": "Add Menu Items to an Existing/New Menu of Window",
      "concept": [
        "addVig2Menu",
        "addVig4Win",
        "addVig4Unix",
        "addNonExisting",
        "addPDF2Vig"
      ],
      "topics": [
        "addVigs2WinMenu"
      ]
    },
    {
      "page": "Aggregate",
      "title": "A Simple Aggregation Mechanism.",
      "topics": [
        "Aggregate"
      ]
    },
    {
      "page": "class.aggregator",
      "title": "A Simple Class for Aggregators",
      "concept": [
        "aggenv",
        "aggfun",
        "initfun"
      ],
      "topics": [
        "aggenv,aggregator-method",
        "aggfun,aggregator-method",
        "aggregator",
        "aggregator-class",
        "class:aggregator",
        "initfun,aggregator-method",
        "initialize,aggregator-method"
      ]
    },
    {
      "page": "class.AnnotatedDataFrame",
      "title": "Class Containing Measured Variables and Their Meta-Data Description.",
      "topics": [
        "$,AnnotatedDataFrame-method",
        "$<-,AnnotatedDataFrame-method",
        "AnnotatedDataFrame",
        "AnnotatedDataFrame,data.frame,data.frame-method",
        "AnnotatedDataFrame,data.frame,missing-method",
        "AnnotatedDataFrame,missing,missing-method",
        "AnnotatedDataFrame-class",
        "class:AnnotatedDataFrame",
        "coerce,AnnotatedDataFrame,data.frame-method",
        "coerce,data.frame,AnnotatedDataFrame-method",
        "combine,AnnotatedDataFrame,AnnotatedDataFrame-method",
        "dim,AnnotatedDataFrame-method",
        "dimLabels",
        "dimLabels,AnnotatedDataFrame-method",
        "dimLabels<-",
        "dimLabels<-,AnnotatedDataFrame,character-method",
        "dimnames,AnnotatedDataFrame-method",
        "dimnames<-,AnnotatedDataFrame-method",
        "featureNames,AnnotatedDataFrame-method",
        "featureNames<-,AnnotatedDataFrame-method",
        "head.AnnotatedDataFrame",
        "initialize,AnnotatedDataFrame-method",
        "ncol,AnnotatedDataFrame-method",
        "pData,AnnotatedDataFrame-method",
        "pData<-,AnnotatedDataFrame,data.frame-method",
        "sampleNames,AnnotatedDataFrame-method",
        "sampleNames<-,AnnotatedDataFrame,ANY-method",
        "show,AnnotatedDataFrame-method",
        "tail.AnnotatedDataFrame",
        "updateObject,AnnotatedDataFrame-method",
        "varLabels,AnnotatedDataFrame-method",
        "varLabels<-,AnnotatedDataFrame-method",
        "varMetadata,AnnotatedDataFrame-method",
        "varMetadata<-,AnnotatedDataFrame,data.frame-method",
        "[,AnnotatedDataFrame-method",
        "[[,AnnotatedDataFrame-method",
        "[[<-,AnnotatedDataFrame-method"
      ]
    },
    {
      "page": "annotatedDataFrameFrom-methods",
      "title": "Methods for Function annotatedDataFrameFrom in Package `Biobase'",
      "topics": [
        "annotatedDataFrameFrom",
        "annotatedDataFrameFrom,AssayData-method",
        "annotatedDataFrameFrom,matrix-method",
        "annotatedDataFrameFrom,NULL-method"
      ]
    },
    {
      "page": "anyMissing",
      "title": "Checks if there are any missing values in an object or not",
      "topics": [
        "anyMissing"
      ]
    },
    {
      "page": "assayData",
      "title": "Retrieve assay data from eSets and ExpressionSets.",
      "topics": [
        "assayData",
        "assayData<-"
      ]
    },
    {
      "page": "class.AssayData",
      "title": "Class \"AssayData\"",
      "topics": [
        "AssayData",
        "assayData,AssayData-method",
        "AssayData-class",
        "assayDataNew",
        "assayDataValidMembers",
        "combine,AssayData,AssayData-method",
        "featureNames,AssayData-method",
        "featureNames<-,AssayData-method",
        "sampleNames,AssayData-method",
        "sampleNames<-,AssayData,ANY-method",
        "sampleNames<-,AssayData,list-method",
        "storageMode,AssayData-method",
        "storageMode<-,AssayData,character-method"
      ]
    },
    {
      "page": "cache",
      "title": "Evaluate an expression if its value is not already cached.",
      "topics": [
        "cache"
      ]
    },
    {
      "page": "channel",
      "title": "Create a new ExpressionSet instance by selecting a specific channel",
      "topics": [
        "channel"
      ]
    },
    {
      "page": "channelNames",
      "title": "Retrieve and set channel names from object",
      "topics": [
        "channelNames",
        "channelNames<-"
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      "page": "copySubstitute",
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      "page": "createPackage",
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        "sample.MultiSet"
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      "page": "description",
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      "page": "dumpPackTxt",
      "title": "Dump Textual Description of a Package",
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      "page": "esApply",
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        "experimentData<-,eSet,MIAME-method",
        "exprs,eSet-method",
        "exprs<-,eSet,AssayData-method",
        "fData,eSet-method",
        "fData<-,eSet,data.frame-method",
        "featureData,eSet-method",
        "featureData<-,eSet,AnnotatedDataFrame-method",
        "featureNames,eSet-method",
        "featureNames<-,eSet-method",
        "fvarLabels,eSet-method",
        "fvarLabels<-,eSet-method",
        "fvarMetadata,eSet-method",
        "fvarMetadata<-,eSet,data.frame-method",
        "initialize,eSet-method",
        "listOrEnv",
        "ncol,eSet-method",
        "notes,eSet-method",
        "notes<-,eSet,ANY-method",
        "pData,eSet-method",
        "pData<-,eSet,data.frame-method",
        "phenoData,eSet-method",
        "phenoData<-,eSet,AnnotatedDataFrame-method",
        "preproc,eSet-method",
        "preproc<-,eSet-method",
        "protocolData,eSet-method",
        "protocolData<-,eSet,character-method",
        "pubMedIds,eSet-method",
        "pubMedIds<-,eSet,character-method",
        "sampleNames,eSet-method",
        "sampleNames<-,eSet,ANY-method",
        "show,eSet-method",
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        "SW",
        "updateObject,eSet-method",
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        "varLabels<-,eSet-method",
        "varMetadata,eSet-method",
        "varMetadata<-,eSet,data.frame-method",
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      "page": "class.ExpressionSet",
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        "write.exprs",
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      "page": "exprs",
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      "page": "featureData",
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      "page": "featureNames",
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      "page": "getPkgVigs",
      "title": "List Vignette Files for a Package",
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      "page": "isCurrent",
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      "page": "lcSuffix",
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      "page": "matchpt",
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      "page": "class.NChannelSet",
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      "page": "notes",
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      "page": "openPDF",
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      "page": "openVignette",
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      "page": "package.version",
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      "page": "phenoData",
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      "page": "readExpressionSet",
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      "page": "data.reporter",
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      "page": "reverseSplit",
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      "page": "rowMedians",
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      "page": "rowQ",
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      "page": "storageMode",
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      "page": "strbreak",
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      "page": "subListExtract",
      "title": "Extract the same element from the sublists of a list",
      "topics": [
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      "page": "testBioCConnection",
      "title": "A function to check internet connectivity to Bioconductor",
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      "page": "updateObjectTo",
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      "page": "updateOldESet",
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      "page": "userQuery",
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      "page": "class.Versioned",
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