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  "Package": "PANR",
  "Type": "Package",
  "Title": "Posterior association networks and functional modules inferred\nfrom rich phenotypes of gene perturbations",
  "Version": "1.59.0",
  "Date": "2012-06-20",
  "Author": "Xin Wang <xin_wang@hms.harvard.edu>",
  "Maintainer": "Xin Wang <xin_wang@hms.harvard.edu>",
  "Description": "This package provides S4 classes and methods for inferring\nfunctional gene networks with edges encoding posterior beliefs\nof gene association types and nodes encoding perturbation\neffects.",
  "License": "Artistic-2.0",
  "Collate": "classUnions.R assoScore.R panGraphics.R AllGenerics.R\nAllClasses.R BetaMixture-methods.R PAN-methods.R",
  "LazyLoad": "yes",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:46 UTC",
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      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
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      "page": "assoScore",
      "title": "Association scores for gene pairs",
      "topics": [
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      ]
    },
    {
      "page": "BetaMixture-class",
      "title": "An S4 class for beta mixture modelling of functional gene associations",
      "topics": [
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        "BetaMixture-class"
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    },
    {
      "page": "buildPAN",
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      "topics": [
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        "buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_missing-method"
      ]
    },
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        "cosineSim"
      ]
    },
    {
      "page": "data-Bakal2007",
      "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens",
      "topics": [
        "Bakal2007",
        "Bakal2007Cluster",
        "bm1",
        "nodeColor"
      ]
    },
    {
      "page": "exportPAN",
      "title": "Export inferred PAN or module graphs to files",
      "topics": [
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        "exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "fitBM",
      "title": "Fit a three-beta mixture model to densities of functional gene associations",
      "topics": [
        "fitBM",
        "fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "fitNULL",
      "title": "Fit the NULL component of a three-beta mixture model for functional gene associations",
      "topics": [
        "fitNULL",
        "fitNULL,BetaMixture,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "infer",
      "title": "Infer a posterior association network",
      "topics": [
        "infer",
        "infer,PAN,list,logical_Or_missing,logical_Or_missing-method"
      ]
    },
    {
      "page": "p2SNR",
      "title": "Translate p-values to Signal-to-Noise Ratios",
      "topics": [
        "p2SNR",
        "p2SNR,BetaMixture,numeric_Or_integer-method"
      ]
    },
    {
      "page": "PAN-class",
      "title": "An S4 class for inferring a posterior association network",
      "topics": [
        "PAN",
        "PAN-class"
      ]
    },
    {
      "page": "pvclustModule",
      "title": "Search enriched functional gene modules by pvclust",
      "topics": [
        "pvclustModule",
        "pvclustModule,PAN,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing,logical_Or_missing-method"
      ]
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      "topics": [
        "sigModules",
        "sigModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
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    },
    {
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        "SNR2p",
        "SNR2p,BetaMixture,numeric_Or_integer-method"
      ]
    },
    {
      "page": "summarize",
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        "summarize,BetaMixture,character_Or_missing-method",
        "summarize,PAN,character_Or_missing-method"
      ]
    },
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        "view,BetaMixture,character_Or_missing-method"
      ]
    },
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      "page": "viewLegend",
      "title": "View the legends for the graph built for PAN",
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        "viewLegend,PAN,character_Or_missing-method"
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    },
    {
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        "viewPAN,PAN,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method"
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