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  "Package": "TreeSummarizedExperiment",
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  "Title": "TreeSummarizedExperiment: a S4 Class for Data with Tree\nStructures",
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  "Date": "2025-03-10",
  "Authors@R": "c(person(\"Ruizhu\", \"Huang\", email = \"ruizhuRH@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3285-1945\")),\nperson(\"Felix G.M.\", \"Ernst\", email = \"felix.gm.ernst@outlook.com\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0000-0001-5064-0928\")),\nperson(given = \"Mark\", family = \"Robinson\", role = c(\"ctb\"),\nemail = \"mark.robinson@mls.uzh.ch\",\ncomment = c(ORCID = \"0000-0002-3048-5518\")),\nperson(given = \"Tuomas\", family = \"Borman\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-8563-8884\")))",
  "Description": "TreeSummarizedExperiment has extended SingleCellExperiment\nto include hierarchical information on the rows or columns of\nthe rectangular data.",
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    "findOS",
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    "isLeaf",
    "joinNode",
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    "makeTSE",
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    "printNode",
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    "referenceSeq",
    "referenceSeq<-",
    "resolveLoop",
    "rowLinks",
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    "rowTree",
    "rowTree<-",
    "rowTreeNames",
    "rowTreeNames<-",
    "shareNode",
    "showNode",
    "signalNode",
    "subsetByLeaf",
    "subsetByNode",
    "toTree",
    "trackNode",
    "transNode",
    "TreeSummarizedExperiment",
    "unionLeaf",
    "updateObject",
    "vertical_slot_names"
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      "fields": [],
      "table": false,
      "tojson": false
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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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        "addLabel"
      ]
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        "aggTSE"
      ]
    },
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      "title": "Perform data aggregations based on the available tree structures",
      "topics": [
        "aggValue"
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      "title": "change internal nodes to leaf nodes",
      "topics": [
        "asLeaf"
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      "topics": [
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      "title": "count the number of leaf nodes",
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        "countLeaf"
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        "countNode"
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    {
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      "title": "Calculate the distance between any two nodes on the tree",
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    {
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      "title": "Find the ancestors of specified nodes",
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      "title": "Find the children",
      "topics": [
        "findChild"
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      "topics": [
        "findDescendant",
        "findOS"
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    {
      "page": "findSibling",
      "title": "find the sibling node",
      "topics": [
        "findSibling"
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      "topics": [
        "isLeaf"
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      "title": "LinkDataFrame: A S4 class extended from DataFrame An S4 class LinkDataFrame",
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      "title": "Construct a LinkDataFrame Construct a LinkDataFrame object",
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        "LinkDataFrame-constructor"
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      "page": "makeTSE",
      "title": "A toy TreeSummarizedExperiment object",
      "topics": [
        "makeTSE"
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    {
      "page": "matTree",
      "title": "Transform a phylo object into a matrix.",
      "topics": [
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      "topics": [
        "printNode"
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      "page": "TreeSummarizedExperiment-combine",
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        "rbind,TreeSummarizedExperiment-method",
        "TreeSummarizedExperiment-combine"
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      "topics": [
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      "title": "An S4 class TreeSummarizedExperiment",
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      "title": "Update a 'TreeSummarizedExperiment' object",
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