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    "integrate_tcr",
    "mergeCloneSizes",
    "overlayLegend",
    "removeLegend",
    "renameApotcRun",
    "RunAPOTC",
    "showCloneHighlight",
    "updateApotc",
    "vizAPOTC"
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      "name": "combined_pbmc",
      "title": "Example Multi-sampled T-cell seurat object with integrated TCR library",
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      "file": "combined_pbmc.rda",
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      ]
    },
    {
      "page": "APOTCPlot",
      "title": "Various variations of visualizations of clonal expansion post-RunAPOTC",
      "topics": [
        "APOTCPlot"
      ]
    },
    {
      "page": "combined_pbmc",
      "title": "Example Multi-sampled T-cell seurat object with integrated TCR library",
      "topics": [
        "combined_pbmc"
      ]
    },
    {
      "page": "containsApotcRun",
      "title": "Check for the existence of an APackOfTheClones run with its run id",
      "topics": [
        "containsApotcRun"
      ]
    },
    {
      "page": "countCloneSizes",
      "title": "count the number of clonotype sizes in a seurat object combined with a VDJ library overall or by cluster",
      "topics": [
        "countCloneSizes"
      ]
    },
    {
      "page": "deleteApotcData",
      "title": "Delete the results of an APackOfTheClones run",
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        "deleteApotcData"
      ]
    },
    {
      "page": "getApotcDataIds",
      "title": "Get all run ids of previous RunAPOTC runs on a seurat object",
      "topics": [
        "getApotcDataIds",
        "getApotcRunIds"
      ]
    },
    {
      "page": "getLastApotcDataId",
      "title": "Get the object id of the most recent RunAPOTC run on a seurat object",
      "topics": [
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        "getLastApotcRunId"
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    },
    {
      "page": "getReductionCentroids",
      "title": "Calculate seurat cluster centroids based on a Dimensional reduction",
      "topics": [
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    },
    {
      "page": "getSharedClones",
      "title": "Compute a list of clonotypes that are shared between seurat clusters",
      "topics": [
        "getSharedClones"
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    },
    {
      "page": "mergeCloneSizes",
      "title": "Merge a list of Clustered Clonotype Frequency Tables",
      "topics": [
        "mergeCloneSizes"
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    },
    {
      "page": "overlayLegend",
      "title": "overlay a clone size legend on an APackOfTheClones plot",
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        "overlayLegend"
      ]
    },
    {
      "page": "removeLegend",
      "title": "Remove current APackOfTheClones legend",
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    },
    {
      "page": "renameApotcRun",
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    {
      "page": "RunAPOTC",
      "title": "Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion",
      "topics": [
        "RunAPOTC"
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    {
      "page": "showCloneHighlight",
      "title": "Highlight specific clones on an APackOfTheClones ggplot",
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    {
      "page": "updateApotc",
      "title": "Update APackOfTheClones objects to the latest format",
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    {
      "page": "vizAPOTC",
      "title": "Directly visualize clonal expansion of a combined seurat object",
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