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    "getMotifsFromSymbol",
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    "getOrthologs",
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    "getSequencesFromGenome",
    "getSimilarityMatrix",
    "getTFclass",
    "getTFclassFromEntrezgene",
    "getTFterms",
    "initBiomart",
    "layout.arc",
    "layout.concentric",
    "plotDegree",
    "plotGraph",
    "plotTRM",
    "plotTRMlegend",
    "processBiogrid",
    "removeVertices",
    "writeTRMreport"
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      "table": false,
      "tojson": false
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    {
      "name": "biogrid_mm",
      "title": "Network dataset of class 'igraph'",
      "object": "biogrid_mm",
      "file": "biogrid_mm.rda",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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    {
      "page": "rTRM-package",
      "title": "Identification transcription regulatory modules (TRMs)",
      "topics": [
        "rTRM-package",
        "rTRM"
      ]
    },
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      "page": "annotateFreq",
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        "annotateFreq"
      ]
    },
    {
      "page": "annotateModule",
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      "topics": [
        "annotateModule"
      ]
    },
    {
      "page": "annotateTRM",
      "title": "Annotate a network object with information about clusters.",
      "topics": [
        "annotateTRM"
      ]
    },
    {
      "page": "biogrid_hs",
      "title": "Network dataset of class 'igraph'",
      "topics": [
        "biogrid_hs"
      ]
    },
    {
      "page": "biogrid_mm",
      "title": "Network dataset of class 'igraph'",
      "topics": [
        "biogrid_mm"
      ]
    },
    {
      "page": "findTRM",
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      "topics": [
        "findTRM"
      ]
    },
    {
      "page": "getAnnotations",
      "title": "Obtain the 'pwm' table fromt the database, containing PWM's annotations.",
      "topics": [
        "getAnnotations"
      ]
    },
    {
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      "topics": [
        "getBiogridData"
      ]
    },
    {
      "page": "getConcentricList",
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      "topics": [
        "getConcentricList"
      ]
    },
    {
      "page": "getLargestComp",
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        "getLargestComp"
      ]
    },
    {
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      "topics": [
        "getMaps"
      ]
    },
    {
      "page": "getMatrices",
      "title": "Obtain a list of PWMs.",
      "topics": [
        "getMatrices"
      ]
    },
    {
      "page": "getMotifsFromEntrezgene",
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      "topics": [
        "getMotifsFromEntrezgene"
      ]
    },
    {
      "page": "getMotifsFromSymbol",
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      "topics": [
        "getMotifsFromSymbol"
      ]
    },
    {
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      "title": "Obtain gene identifiers for a target organism associated with a list of PWMs.",
      "topics": [
        "getOrthologFromMatrix"
      ]
    },
    {
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      "title": "Obtain the mapping to Entrez Gene identifiers in the given organism.",
      "topics": [
        "getOrthologs"
      ]
    },
    {
      "page": "getOrthologsFromBiomart",
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      "topics": [
        "getOrthologsFromBiomart"
      ]
    },
    {
      "page": "getSequencesFromGenome",
      "title": "Retrieves a set of sequences from a BSgenome object and optionally appends a label to each sequence id.",
      "topics": [
        "getSequencesFromGenome"
      ]
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        "getSimilarityMatrix"
      ]
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      "page": "getTFclass",
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      "topics": [
        "getTFclass"
      ]
    },
    {
      "page": "getTFclassFromEntrezgene",
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      "topics": [
        "getTFclassFromEntrezgene"
      ]
    },
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      ]
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    {
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      "title": "Plot the legend of a TRM with information about the cluster families.",
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        "Case study: TRM associated with Sox2 in embryonic stem cells (ESCs)",
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