{
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  "Title": "Platform Design Information Package Builder",
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  "Author": "Seth Falcon, Vince Carey, Matt Settles, Kristof de Beuf,\nBenilton Carvalho",
  "Maintainer": "Benilton Carvalho <benilton@unicamp.br>",
  "LazyLoad": "yes",
  "License": "Artistic-2.0",
  "Collate": "AllClasses.R AllGenerics.R initialize-methods.R utils.R\nschema.R initDb.R initDb.snp6.R pmmmBlockToMat.R loaders.R\nloaders.snp6.R makePdInfoPackage-methods.R chipName-methods.R\ngetGeometry-methods.R pdBuilderV2TiledRegion.R\npdBuilderV2ExonTranscription.R pdBuilderV2Gene.R\npdBuilderV2HTA2.R pdBuilderV2AffyTiling.R\npdBuilderV2NgsExpression.R pdBuilderV2AffyExpressionHT.R\npdBuilderV2AffySNP.R pdBuilderV2AffySNPCNV.R pdBuilderV2miRNA.R\npdBuilderV3GenericArray.R pdBuilderV2Clariom.R",
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  "Date/Publication": "2026-04-28 12:32:07 UTC",
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    "warning": 5,
    "note": 15
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    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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      "page": "AffyClariomSPDInfoPkgSeed-class",
      "title": "Class \"AffyClariomSPDInfoPkgSeed\"",
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        "AffyClariomSPDInfoPkgSeed-class"
      ]
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      "page": "AffyExpressionPDInfoPkgSeed-class",
      "title": "Class \"AffyExpressionPDInfoPkgSeed\"",
      "topics": [
        "AffyExpressionPDInfoPkgSeed-class"
      ]
    },
    {
      "page": "AffySNPCNVPDInfoPkgSeed-class",
      "title": "Class \"AffySNPCNVPDInfoPkgSeed\"",
      "topics": [
        "AffySNPCNVPDInfoPkgSeed-class"
      ]
    },
    {
      "page": "AffySNPCNVPDInfoPkgSeed2-class",
      "title": "Class \"AffySNPCNVPDInfoPkgSeed2\"",
      "topics": [
        "AffySNPCNVPDInfoPkgSeed2-class"
      ]
    },
    {
      "page": "AffySNPPDInfoPkgSeed-class",
      "title": "Class \"AffySNPPDInfoPkgSeed\"",
      "topics": [
        "AffySNPPDInfoPkgSeed-class"
      ]
    },
    {
      "page": "AffySNPPDInfoPkgSeed2-class",
      "title": "Class \"AffySNPPDInfoPkgSeed2\"",
      "topics": [
        "AffySNPPDInfoPkgSeed2-class"
      ]
    },
    {
      "page": "AffySTPDInfoPkgSeed-class",
      "title": "Class \"AffySTPDInfoPkgSeed\" for the Sense Target gene-level array",
      "topics": [
        "AffyExonPDInfoPkgSeed-class",
        "AffyGenePDInfoPkgSeed-class"
      ]
    },
    {
      "page": "AffyTilingPDInfoPkgSeed-class",
      "title": "Class \"AffyTilingPDInfoPkgSeed\"",
      "topics": [
        "AffyTilingPDInfoPkgSeed-class"
      ]
    },
    {
      "page": "GenericArrayFunctions",
      "title": "Helper functions to assist the creation of an annotation package for a generic array",
      "topics": [
        "cdf2table",
        "sequenceParser"
      ]
    },
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      "page": "chipName",
      "title": "Return an Official Chip/Platform Name",
      "topics": [
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        "chipName,AffyExpressionPDInfoPkgSeed-method",
        "chipName,AffyGeneric1PDInfoPkgSeed-method",
        "chipName,AffySNPCNVPDInfoPkgSeed-method",
        "chipName,AffySNPCNVPDInfoPkgSeed2-method",
        "chipName,AffySNPPDInfoPkgSeed-method",
        "chipName,AffySNPPDInfoPkgSeed2-method",
        "chipName,AffySTPDInfoPkgSeed-method",
        "chipName,AffyTilingPDInfoPkgSeed-method",
        "chipName,NimbleGenPDInfoPkgSeed-method"
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      "page": "getGeometry",
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        "getGeometry,AffyExpressionPDInfoPkgSeed-method",
        "getGeometry,AffySNPCNVPDInfoPkgSeed-method",
        "getGeometry,AffySNPPDInfoPkgSeed-method",
        "getGeometry,AffySTPDInfoPkgSeed-method",
        "getGeometry,AffyTilingPDInfoPkgSeed-method",
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        "makePdInfoPackage,AffyClariomSPDInfoPkgSeed-method",
        "makePdInfoPackage,AffyExonPDInfoPkgSeed-method",
        "makePdInfoPackage,AffyExpressionPDInfoPkgSeed-method",
        "makePdInfoPackage,AffyGenePDInfoPkgSeed-method",
        "makePdInfoPackage,AffyHTAPDInfoPkgSeed-method",
        "makePdInfoPackage,AffyMiRNAPDInfoPkgSeed-method",
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