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      "page": "getDEE2",
      "title": "getDEE2: Programmatic access to the DEE2 RNA expression dataset",
      "topics": [
        "getDEE2"
      ]
    },
    {
      "page": "getDEE2_bundle",
      "title": "Get a DEE2 project bundle",
      "topics": [
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    {
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      "title": "Get DEE2 Metadata",
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