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    "RedPort",
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      "class": [
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      "tojson": false
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        "addEdges,character-method",
        "addEdges,data.frame-method"
      ]
    },
    {
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      "title": "Adding 'igraph' objects to RedeR",
      "topics": [
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        "addGraph,RedPort-method"
      ]
    },
    {
      "page": "addGraphToRedeR",
      "title": "Adding 'igraph' objects to RedeR",
      "topics": [
        "addGraphToRedeR"
      ]
    },
    {
      "page": "addLegendToRedeR",
      "title": "Adding graph legends to the RedeR app",
      "topics": [
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      ]
    },
    {
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      "title": "addNodes",
      "topics": [
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        "addNodes,character-method"
      ]
    },
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      "title": "Call RedeR app from R",
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        "calld,RedPort-method"
      ]
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      "title": "deleteEdges",
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        "deleteEdges,character-method",
        "deleteEdges,data.frame-method"
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        "deleteNodes,character-method"
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        "exitd,RedPort-method"
      ]
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    {
      "page": "exitRedeR",
      "title": "Exit the RedeR R-to-Java interface",
      "topics": [
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      ]
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        "getGraph,RedPort-method"
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      "topics": [
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