{
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  "Package": "Pigengene",
  "Type": "Package",
  "Title": "Infers biological signatures from gene expression data",
  "Version": "1.39.0",
  "Date": "2016-03-31",
  "Author": "Habil Zare, Amir Foroushani, Rupesh Agrahari, Meghan Short,\nIsha Mehta, Neda Emami, and Sogand Sajedi",
  "Maintainer": "Habil Zare <zare@u.washington.edu>",
  "biocViews": "GeneExpression, RNASeq, NetworkInference, Network,\nGraphAndNetwork, BiomedicalInformatics, SystemsBiology,\nTranscriptomics, Classification, Clustering, DecisionTree,\nDimensionReduction, PrincipalComponent, Microarray,\nNormalization, ImmunoOncology",
  "Description": "Pigengene package provides an efficient way to infer\nbiological signatures from gene expression profiles. The\nsignatures are independent from the underlying platform, e.g.,\nthe input can be microarray or RNA Seq data. It can even infer\nthe signatures using data from one platform, and evaluate them\non the other. Pigengene identifies the modules (clusters) of\nhighly coexpressed genes using coexpression network analysis,\nsummarizes the biological information of each module in an\neigengene, learns a Bayesian network that models the\nprobabilistic dependencies between modules, and builds a\ndecision tree based on the expression of eigengenes.",
  "License": "GPL (>=2)",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:36 UTC",
  "RemoteUrl": "https://github.com/bioc/Pigengene",
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  "Packaged": {
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  "_created": "2026-10-15T09:06:00.000Z",
  "_published": "2026-10-15T09:47:11.749Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38709468618",
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  "_upstream": "https://github.com/bioc/Pigengene",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "message.if",
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    "one.step.pigengene",
    "pheatmap.type",
    "plot.pigengene",
    "preds.at",
    "project.eigen",
    "pvalues.manova",
    "save.if",
    "wgcna.one.step"
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      "title": "AML gene expression profile",
      "object": "aml",
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        "array"
      ],
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      "rows": 202,
      "table": true,
      "tojson": true
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      "title": "Eigengenes of 33 modules",
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      "table": false,
      "tojson": true
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        "array"
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      "rows": 164,
      "table": true,
      "tojson": true
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    {
      "name": "pigengene",
      "title": "An object of class 'Pigengene'",
      "object": "pigengene",
      "file": "pigengene.RData",
      "class": [
        "pigengene"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "Pigengene-package",
      "title": "Infers robust biological signatures from gene expression data",
      "topics": [
        "Pigengene-package",
        "Pigengene"
      ]
    },
    {
      "page": "aml",
      "title": "AML gene expression profile",
      "topics": [
        "aml"
      ]
    },
    {
      "page": "apply.filter",
      "title": "Applies a given filter on the data",
      "topics": [
        "apply.filter"
      ]
    },
    {
      "page": "balance",
      "title": "Balances the number of samples",
      "topics": [
        "balance"
      ]
    },
    {
      "page": "calculate.beta",
      "title": "Estimates an appropriate power value",
      "topics": [
        "calculate.beta"
      ]
    },
    {
      "page": "check.nas",
      "title": "Removes 'NA's from a data matrix",
      "topics": [
        "check.nas"
      ]
    },
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      "page": "check.pigengene.input",
      "title": "Quality check on the imput",
      "topics": [
        "check.pigengene.input"
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    {
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      "title": "Combines two or more networks",
      "topics": [
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    },
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      "page": "compact.tree",
      "title": "Reduces the number of genes in a decision tree",
      "topics": [
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    {
      "page": "compute.pigengene",
      "title": "Computes the eigengenes",
      "topics": [
        "compute.pigengene"
      ]
    },
    {
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      "title": "Computes distance correlation for give matrix",
      "topics": [
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      ]
    },
    {
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      "title": "Identifies modules of the network",
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      "title": "Draws a Bayesian network",
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      "title": "Eigengenes of 33 modules",
      "topics": [
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      "title": "Maps gene IDs",
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        "get.genes"
      ]
    },
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      "page": "get.used.features",
      "title": "Return the features used in a tree",
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    {
      "page": "pigengene",
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        "2 How to run Pigengene ?",
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      "created": "2016-05-26 12:35:24",
      "modified": "2021-10-14 16:10:53",
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