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  "Title": "TreeSummarizedExperiment: a S4 Class for Data with Tree\nStructures",
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  "Date": "2025-03-10",
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  "Description": "TreeSummarizedExperiment has extended SingleCellExperiment\nto include hierarchical information on the rows or columns of\nthe rectangular data.",
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    "aggValue",
    "asLeaf",
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    "colLinks",
    "colnames<-",
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    "makeTSE",
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    "printNode",
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    "shareNode",
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      "title": "The 'TreeSummarizedExperiment' package",
      "topics": [
        "TreeeSummarizedExperiment-package"
      ]
    },
    {
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      "title": "add labels to nodes of a tree",
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      "title": "Perform data aggregations based on the available tree structures",
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      "title": "Perform data aggregations based on the available tree structures",
      "topics": [
        "aggValue"
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    },
    {
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      "title": "change internal nodes to leaf nodes",
      "topics": [
        "asLeaf"
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      "title": "Convert a data frame to a phylo object",
      "topics": [
        "asPhylo"
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    },
    {
      "page": "changeTree",
      "title": "Change the row or column tree",
      "topics": [
        "changeTree"
      ]
    },
    {
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      "title": "count the number of leaf nodes",
      "topics": [
        "countLeaf"
      ]
    },
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      "title": "count the number of nodes",
      "topics": [
        "countNode"
      ]
    },
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      "title": "Detect loops 'detectLoop' detects loops",
      "topics": [
        "detectLoop"
      ]
    },
    {
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      "title": "Calculate the distance between any two nodes on the tree",
      "topics": [
        "distNode"
      ]
    },
    {
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      "title": "Find the ancestors of specified nodes",
      "topics": [
        "findAncestor"
      ]
    },
    {
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      "title": "Find the children",
      "topics": [
        "findChild"
      ]
    },
    {
      "page": "findDescendant",
      "title": "Find descendants (or offsprings)",
      "topics": [
        "findDescendant",
        "findOS"
      ]
    },
    {
      "page": "findSibling",
      "title": "find the sibling node",
      "topics": [
        "findSibling"
      ]
    },
    {
      "page": "isLeaf",
      "title": "To test whether the specified nodes are leaf nodes",
      "topics": [
        "isLeaf"
      ]
    },
    {
      "page": "LinkDataFrame-class",
      "title": "LinkDataFrame: A S4 class extended from DataFrame An S4 class LinkDataFrame",
      "topics": [
        "LinkDataFrame-class"
      ]
    },
    {
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      "title": "Construct a LinkDataFrame Construct a LinkDataFrame object",
      "topics": [
        "LinkDataFrame",
        "LinkDataFrame-constructor"
      ]
    },
    {
      "page": "makeTSE",
      "title": "A toy TreeSummarizedExperiment object",
      "topics": [
        "makeTSE"
      ]
    },
    {
      "page": "matTree",
      "title": "Transform a phylo object into a matrix.",
      "topics": [
        "matTree"
      ]
    },
    {
      "page": "printNode",
      "title": "To print out the node labels",
      "topics": [
        "printNode"
      ]
    },
    {
      "page": "TreeSummarizedExperiment-combine",
      "title": "Combine TSEs by rows or columns",
      "topics": [
        "cbind,TreeSummarizedExperiment-method",
        "rbind,TreeSummarizedExperiment-method",
        "TreeSummarizedExperiment-combine"
      ]
    },
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      "title": "Resolve loops 'resolveLoop' resolve loops by adding suffix to the child node. The suffix is \"_i\" where 'i' is a number. Please see examples.",
      "topics": [
        "resolveLoop"
      ]
    },
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      "title": "TreeSummarizedExperiment-accessors",
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        "colLinks",
        "colLinks,TreeSummarizedExperiment-method",
        "colnames<-,TreeSummarizedExperiment-method",
        "colTree",
        "colTree,TreeSummarizedExperiment-method",
        "colTree<-",
        "colTree<-,TreeSummarizedExperiment-method",
        "colTreeNames",
        "colTreeNames,TreeSummarizedExperiment-method",
        "colTreeNames<-",
        "colTreeNames<-,TreeSummarizedExperiment-method",
        "referenceSeq",
        "referenceSeq,TreeSummarizedExperiment-method",
        "referenceSeq<-",
        "referenceSeq<-,TreeSummarizedExperiment-method",
        "rowLinks",
        "rowLinks,TreeSummarizedExperiment-method",
        "rownames<-,TreeSummarizedExperiment-method",
        "rowTree",
        "rowTree,TreeSummarizedExperiment-method",
        "rowTree<-",
        "rowTree<-,TreeSummarizedExperiment-method",
        "rowTreeNames",
        "rowTreeNames,TreeSummarizedExperiment-method",
        "rowTreeNames<-",
        "rowTreeNames<-,TreeSummarizedExperiment-method",
        "subsetByLeaf",
        "subsetByLeaf,TreeSummarizedExperiment-method",
        "subsetByNode",
        "subsetByNode,TreeSummarizedExperiment-method",
        "TreeSummarizedExperiment-accessor",
        "[,TreeSummarizedExperiment,ANY,ANY,ANY-method",
        "[<-,TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "shareNode",
      "title": "Find the share node",
      "topics": [
        "shareNode"
      ]
    },
    {
      "page": "showNode",
      "title": "Find nodes on the tree",
      "topics": [
        "showNode"
      ]
    },
    {
      "page": "joinNode",
      "title": "Join nodes",
      "topics": [
        "joinNode",
        "signalNode"
      ]
    },
    {
      "page": "tinyTree",
      "title": "A simulated phylogenetic tree with 10 tips and 9 internal nodes",
      "topics": [
        "tinyTree"
      ]
    },
    {
      "page": "toTree",
      "title": "Translate a data frame to a phylo object",
      "topics": [
        "toTree"
      ]
    },
    {
      "page": "trackNode",
      "title": "track the nodes of a phylo tree",
      "topics": [
        "trackNode"
      ]
    },
    {
      "page": "convertNode",
      "title": "Transfer between node number and node label",
      "topics": [
        "convertNode",
        "transNode"
      ]
    },
    {
      "page": "TreeSummarizedExperiment-class",
      "title": "An S4 class TreeSummarizedExperiment",
      "topics": [
        "TreeSummarizedExperiment-class"
      ]
    },
    {
      "page": "TreeSummarizedExperiment-constructor",
      "title": "Construct a TreeSummarizedExperiment object",
      "topics": [
        "TreeSummarizedExperiment",
        "TreeSummarizedExperiment-constructor"
      ]
    },
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