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  "Description": "This package is a pipeline to identify the key gene\nregulators in a biological process, for example in cell\ndifferentiation and in cell development after stimulation.\nThere are four major steps in this pipeline: (1) differential\nexpression analysis; (2) regulator-target network inference;\n(3) enrichment analysis; and (4) regulators scoring and\nranking.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-09 17:08:07 UTC",
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  "Author": "Weiyang Tao [cre, aut],\nAridaman Pandit [aut]",
  "Maintainer": "Weiyang Tao <weiyangtao1513@gmail.com>",
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    "results_topNet",
    "show",
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      "page": "DeaSet-class",
      "title": "DeaSet class",
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      "title": "dimention of `TopNetwork` object",
      "topics": [
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    {
      "page": "Enrich-class",
      "title": "Enrich class",
      "topics": [
        "Enrich-class"
      ]
    },
    {
      "page": "getResultsNames",
      "title": "Inference the name of results of DESeq analysis by a formula (or model matrix) and sample information",
      "topics": [
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      ]
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    {
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      "title": "head or tail of Score object",
      "topics": [
        "head,Score-method",
        "tail,Score-method"
      ]
    },
    {
      "page": "Lyme_GSE63085",
      "title": "Example RNAseq dataset [Human]",
      "topics": [
        "Lyme_GSE63085"
      ]
    },
    {
      "page": "newDeaSet",
      "title": "DeaSet object creator",
      "topics": [
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    {
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      "title": "TopNetwork object creator",
      "topics": [
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      "title": "Plot results of FET/GSEA enrichment analysis",
      "topics": [
        "plot_Enrich",
        "plot_Enrich,RegenrichSet-method"
      ]
    },
    {
      "page": "plotOrders",
      "title": "Compare the orders of two vectors",
      "topics": [
        "plotOrders"
      ]
    },
    {
      "page": "plotRegTarExpr",
      "title": "Plot regulator and its targets expression",
      "topics": [
        "plotRegTarExpr"
      ]
    },
    {
      "page": "plotSoftPower",
      "title": "Plot soft power for WGCNA analysis",
      "topics": [
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      ]
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    {
      "page": "print.Score",
      "title": "Print Score object",
      "topics": [
        "print.Score"
      ]
    },
    {
      "page": "regenrich_diffExpr",
      "title": "Differential expression analysis step",
      "topics": [
        "regenrich_diffExpr",
        "regenrich_diffExpr,RegenrichSet-method"
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    {
      "page": "regenrich_enrich",
      "title": "Enrichment analysis step",
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        "regenrich_enrich,RegenrichSet-method"
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    },
    {
      "page": "regenrich_network",
      "title": "Regulator-target network inference step",
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        "regenrich_network,RegenrichSet-method",
        "regenrich_network<-",
        "regenrich_network<-,RegenrichSet,data.frame-method",
        "regenrich_network<-,RegenrichSet,TopNetwork-method"
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        "regenrich_rankScore,RegenrichSet-method"
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      "topics": [
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        "results_topNet"
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}