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  "Title": "Classify diseases and build associated gene networks using gene\nexpression profiles",
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  "Author": "Sara Aibar, Celia Fontanillo and Javier De Las Rivas.\nBioinformatics and Functional Genomics Group. Cancer Research\nCenter (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.",
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    "numSignificantGenes",
    "overview",
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    "plot.GenesRanking",
    "plot.GeNetClassifierReturn",
    "plotAssignments",
    "plotDiscriminantPower",
    "plotExpressionProfiles",
    "plotNetwork",
    "queryGeNetClassifier",
    "querySummary",
    "setProperties",
    "show"
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      ],
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      "object": "leukemiasClassifier",
      "file": "leukemiasClassifier.RData",
      "class": [
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      "page": "geNetClassifier-package",
      "title": "classify diseases and build associated gene networks using gene expression profiles",
      "topics": [
        "geNetClassifier-package"
      ]
    },
    {
      "page": "calculateGenesRanking",
      "title": "Calculate GenesRanking",
      "topics": [
        "calculateGenesRanking"
      ]
    },
    {
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      "title": "Probability matrix.",
      "topics": [
        "externalValidation.probMatrix"
      ]
    },
    {
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      "title": "Statistics of the external validation.",
      "topics": [
        "externalValidation.stats"
      ]
    },
    {
      "page": "gClasses-methods",
      "title": "Classes in the ranking.",
      "topics": [
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        "gClasses,GenesRanking-method",
        "gClasses-methods"
      ]
    },
    {
      "page": "GeneralizationError-class",
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        "GeneralizationError-class",
        "initialize,GeneralizationError-method",
        "show,GeneralizationError-method"
      ]
    },
    {
      "page": "genesDetails-methods",
      "title": "Details of the genes in the network.",
      "topics": [
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        "genesDetails,GenesRanking-method",
        "genesDetails-methods",
        "genesDetails.GenesRanking"
      ]
    },
    {
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      "title": "Class \"GenesNetwork\"",
      "topics": [
        "GenesNetwork",
        "GenesNetwork-class",
        "initialize,GenesNetwork-method",
        "show,GenesNetwork-method"
      ]
    },
    {
      "page": "GenesRanking-class",
      "title": "Class \"GenesRanking\"",
      "topics": [
        "extractGenes,GenesRanking-method",
        "GenesRanking",
        "GenesRanking-class",
        "initialize,GenesRanking-method",
        "show,GenesRanking-method"
      ]
    },
    {
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      "title": "Gene symbols associated to human Ensemble IDs.",
      "topics": [
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      ]
    },
    {
      "page": "geNetClassifier",
      "title": "Main function of the geNetClassifier package. Trains the multi-class SVM classifier based on the given gene expression data through transparent detection of gene markers and their associated networks.",
      "topics": [
        "geNetClassifier"
      ]
    },
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      "title": "Class \"GeNetClassifierReturn\"",
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        "GeNetClassifierReturn",
        "GeNetClassifierReturn-class",
        "getSlots,GeNetClassifierReturn-method",
        "initialize,GeNetClassifierReturn-method",
        "names,GeNetClassifierReturn-method",
        "show,GeNetClassifierReturn-method"
      ]
    },
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      "title": "Edges in the network.",
      "topics": [
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        "getEdges",
        "getEdges,GenesNetwork-method",
        "getEdges-methods"
      ]
    },
    {
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      "title": "Nodes in the network.",
      "topics": [
        "getNodes",
        "getNodes,GenesNetwork-method",
        "getNodes-methods",
        "nodes,GenesNetwork-method"
      ]
    },
    {
      "page": "getNumEdges-methods",
      "title": "Number of edges in the network.",
      "topics": [
        "getNumEdges",
        "getNumEdges,GenesNetwork-method",
        "getNumEdges-methods",
        "numEdges,GenesNetwork-method"
      ]
    },
    {
      "page": "getNumNodes-methods",
      "title": "Number of nodes in the network.",
      "topics": [
        "getNumNodes",
        "getNumNodes,GenesNetwork-method",
        "getNumNodes-methods",
        "numNodes,GenesNetwork-method"
      ]
    },
    {
      "page": "getRanking-methods",
      "title": "Shows the genes ranking.",
      "topics": [
        "getRanking",
        "getRanking,GenesRanking-method",
        "getRanking-methods",
        "getRanking.GenesRanking"
      ]
    },
    {
      "page": "getSubNetwork-methods",
      "title": "Get a sub-network.",
      "topics": [
        "getSubNetwork",
        "getSubNetwork,GenesNetwork-method",
        "getSubNetwork,GeNetClassifierReturn-method",
        "getSubNetwork,list-method",
        "getSubNetwork,NULL-method",
        "getSubNetwork-methods"
      ]
    },
    {
      "page": "getTopRanking-methods",
      "title": "Gets a new ranking with the given top genes.",
      "topics": [
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        "getTopRanking,GenesRanking-method",
        "getTopRanking-methods",
        "getTopRanking.GenesRanking"
      ]
    },
    {
      "page": "leukemiasClassifier",
      "title": "Sample leukemias classifier",
      "topics": [
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      ]
    },
    {
      "page": "network2txt",
      "title": "network2txt",
      "topics": [
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        "network2txt,GenesNetwork-method",
        "network2txt,list-method",
        "network2txt-methods"
      ]
    },
    {
      "page": "numGenes-methods",
      "title": "Number of genes in the genesRanking.",
      "topics": [
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        "numGenes,GenesRanking-method",
        "numGenes-methods"
      ]
    },
    {
      "page": "numSignificantGenes-methods",
      "title": "Number of ranked genes over the posterior probability threshold.",
      "topics": [
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        "numSignificantGenes,GenesRanking-method",
        "numSignificantGenes-methods",
        "numSignificantGenes.GenesRanking"
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        "overview,GeneralizationError-method",
        "overview,GenesNetwork-method",
        "overview,GenesRanking-method",
        "overview,GeNetClassifierReturn-method",
        "overview-methods"
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      "topics": [
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        "plotGenesRanking"
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        "plot.GeNetClassifierReturn",
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        "plotGeNetClassifierReturn,GeNetClassifierReturn-method"
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      "topics": [
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    },
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      "topics": [
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      "topics": [
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        "plot.GenesNetwork",
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      "title": "Summary of the query.",
      "topics": [
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      "page": "setProperties-methods",
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