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  "Package": "decode",
  "Title": "Differential Co-Expression and Differential Expression Analysis",
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  "Authors@R": "person(\"Thomas\", \"Lui\", , \"tlui27@yahoo.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Integrated differential expression (DE) and differential\nco-expression (DC) analysis on gene expression data based on\nDECODE (DifferEntial CO-expression and Differential Expression)\nalgorithm.",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
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  "Packaged": {
    "Date": "2026-05-18 06:11:18 UTC",
    "User": "root"
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  "Author": "Thomas Lui [aut, cre]",
  "Maintainer": "Thomas Lui <tlui27@yahoo.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2015-07-13 00:00:00 UTC",
  "RemoteUrl": "https://github.com/cran/decode",
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    "author": "Thomas Lui <tlui27@yahoo.com>",
    "committer": "Gabor Csardi <csardi.gabor@gmail.com>",
    "message": "version 1.2\n",
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    "extra/citation.json",
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  "_exports": [
    "getAssoGeneSetPValue",
    "getBestAssociatedGeneSet",
    "getBonferroniPValue",
    "getDE_DC_OptimalThreshold",
    "getFDR",
    "getPartitionIndex",
    "getPathway",
    "openFileToWrite",
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    {
      "page": "getAssoGeneSetPValue",
      "title": "Calculate the p-value between selected genes and functional gene set",
      "topics": [
        "getAssoGeneSetPValue"
      ]
    },
    {
      "page": "getBestAssociatedGeneSet",
      "title": "Get best associated functional gene sets for partitions of gene i",
      "topics": [
        "getBestAssociatedGeneSet"
      ]
    },
    {
      "page": "getBonferroniPValue",
      "title": "Adjust p-value by Bonferroni correction",
      "topics": [
        "getBonferroniPValue"
      ]
    },
    {
      "page": "getDE_DC_OptimalThreshold",
      "title": "Perform chi-square optimization",
      "topics": [
        "getDE_DC_OptimalThreshold"
      ]
    },
    {
      "page": "getFDR",
      "title": "Adjust p-value by Benjamini and Hochberg method",
      "topics": [
        "getFDR"
      ]
    },
    {
      "page": "getPartitionIndex",
      "title": "Get gene index of 8 partitions for gene i",
      "topics": [
        "getPartitionIndex"
      ]
    },
    {
      "page": "getPathway",
      "title": "read functional gene sets",
      "topics": [
        "getPathway"
      ]
    },
    {
      "page": "openFileToWrite",
      "title": "Open file to write result",
      "topics": [
        "openFileToWrite"
      ]
    },
    {
      "page": "runDecode",
      "title": "Differential Co-Expression and Differential Expression Analysis",
      "topics": [
        "runDecode"
      ]
    },
    {
      "page": "sumResult_MinGain",
      "title": "Summarize the functional gene set results into text file",
      "topics": [
        "sumResult_MinGain"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "v.Rmd",
      "filename": "v.html",
      "title": "Differential Co-Expression and Differential Expression Analysis",
      "author": "Thomas Lui",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Package description",
        "Reference",
        "Input gene expression data format",
        "Input gene set data format",
        "To load the package:",
        "Example 1:",
        "Example 2:"
      ],
      "created": "2015-03-17",
      "modified": "2015-07-13",
      "commits": 2
    }
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