{
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  "Package": "compcodeR",
  "Type": "Package",
  "Title": "RNAseq data simulation, differential expression analysis and\nperformance comparison of differential expression methods",
  "Version": "1.49.0",
  "Authors@R": "c(\nperson(\"Charlotte\", \"Soneson\", role = c(\"aut\", \"cre\"),\nemail = \"charlottesoneson@gmail.com\", comment = c(ORCID = \"0000-0003-3833-2169\")),\nperson(\"Paul\", \"Bastide\", role = \"aut\",\nemail = \"paul.bastide@umontpellier.fr\", comment = c(ORCID = \"0000-0002-8084-9893\")),\nperson(\"Mélina\", \"Gallopin\", role = \"aut\",\nemail = \"melina.gallopin@u-psud.fr\", comment = c(ORCID = \"0000-0002-2431-7825 \"))\n)",
  "Description": "This package provides extensive functionality for\ncomparing results obtained by different methods for\ndifferential expression analysis of RNAseq data. It also\ncontains functions for simulating count data. Finally, it\nprovides convenient interfaces to several packages for\nperforming the differential expression analysis. These can also\nbe used as templates for setting up and running a user-defined\ndifferential analysis workflow within the framework of the\npackage.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, RNASeq, DifferentialExpression",
  "RoxygenNote": "7.2.3",
  "URL": "https://github.com/csoneson/compcodeR",
  "BugReports": "https://github.com/csoneson/compcodeR/issues",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:02 UTC",
  "RemoteUrl": "https://github.com/bioc/compcodeR",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:39:14 UTC",
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  "Author": "Charlotte Soneson [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3833-2169>),\nPaul Bastide [aut] (ORCID: <https://orcid.org/0000-0002-8084-9893>),\nMélina Gallopin [aut] (ORCID: <https://orcid.org/0000-0002-2431-7825>)",
  "Maintainer": "Charlotte Soneson <charlottesoneson@gmail.com>",
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  "_created": "2026-05-31T06:39:14.000Z",
  "_published": "2026-05-31T07:43:28.401Z",
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  "_realowner": "bioc",
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  "_exports": [
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    "check_compData_results",
    "check_phyloCompData",
    "checkDataObject",
    "checkTableConsistency",
    "compData",
    "convertcompDataToList",
    "convertListTocompData",
    "convertListTophyloCompData",
    "convertphyloCompDataToList",
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    "DESeq2.length.createRmd",
    "DSS.createRmd",
    "EBSeq.createRmd",
    "edgeR.exact.createRmd",
    "edgeR.GLM.createRmd",
    "generateCodeHTMLs",
    "generateSyntheticData",
    "lengthNorm.limma.createRmd",
    "lengthNorm.sva.limma.createRmd",
    "listcreateRmd",
    "logcpm.limma.createRmd",
    "NBPSeq.createRmd",
    "NOISeq.prenorm.createRmd",
    "phyloCompData",
    "phylolm.createRmd",
    "runComparison",
    "runComparisonGUI",
    "runComparisonShiny",
    "runDiffExp",
    "sqrtcpm.limma.createRmd",
    "summarizeSyntheticDataSet",
    "TCC.createRmd",
    "ttest.createRmd",
    "voom.limma.createRmd",
    "voom.ttest.createRmd"
  ],
  "_help": [
    {
      "page": "compcodeR-package",
      "title": "RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods",
      "topics": [
        "compcodeR-package",
        "compcodeR"
      ]
    },
    {
      "page": "check_compData",
      "title": "Check the validity of a 'compData' object",
      "topics": [
        "check_compData"
      ]
    },
    {
      "page": "check_compData_results",
      "title": "Check the validity of a 'compData' result object",
      "topics": [
        "check_compData_results"
      ]
    },
    {
      "page": "check_phyloCompData",
      "title": "Check the validity of a 'phyloCompData' object",
      "topics": [
        "check_phyloCompData"
      ]
    },
    {
      "page": "checkDataObject",
      "title": "Check a list or a 'compData' object for compatibility with the differential expression functions interfaced by 'compcodeR'",
      "topics": [
        "checkDataObject"
      ]
    },
    {
      "page": "checkTableConsistency",
      "title": "Check consistency of input table to 'runComparison'",
      "topics": [
        "checkTableConsistency"
      ]
    },
    {
      "page": "compData",
      "title": "Create a 'compData' object",
      "topics": [
        "compData"
      ]
    },
    {
      "page": "compData-class",
      "title": "Class compData",
      "topics": [
        "compData-class"
      ]
    },
    {
      "page": "convertcompDataToList",
      "title": "Convert a 'compData' object to a list",
      "topics": [
        "convertcompDataToList"
      ]
    },
    {
      "page": "convertListTocompData",
      "title": "Convert a list with data and results to a 'compData' object",
      "topics": [
        "convertListTocompData"
      ]
    },
    {
      "page": "convertListTophyloCompData",
      "title": "Convert a list with data and results to a 'phyloCompData' object",
      "topics": [
        "convertListTophyloCompData"
      ]
    },
    {
      "page": "convertphyloCompDataToList",
      "title": "Convert a 'phyloCompData' object to a list",
      "topics": [
        "convertphyloCompDataToList"
      ]
    },
    {
      "page": "DESeq2.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2",
      "topics": [
        "DESeq2.createRmd"
      ]
    },
    {
      "page": "DESeq2.length.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2 with custom model matrix",
      "topics": [
        "DESeq2.length.createRmd"
      ]
    },
    {
      "page": "DSS.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with DSS",
      "topics": [
        "DSS.createRmd"
      ]
    },
    {
      "page": "EBSeq.createRmd",
      "title": "Generate a .Rmd file containing code to perform differential expression analysis with EBSeq",
      "topics": [
        "EBSeq.createRmd"
      ]
    },
    {
      "page": "edgeR.exact.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR exact test",
      "topics": [
        "edgeR.exact.createRmd"
      ]
    },
    {
      "page": "edgeR.GLM.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR GLM approach",
      "topics": [
        "edgeR.GLM.createRmd"
      ]
    },
    {
      "page": "generateCodeHTMLs",
      "title": "Generate HTML file(s) containing code used to run differential expression analysis.",
      "topics": [
        "generateCodeHTMLs"
      ]
    },
    {
      "page": "generateSyntheticData",
      "title": "Generate synthetic count data sets",
      "topics": [
        "generateSyntheticData"
      ]
    },
    {
      "page": "lengthNorm.limma.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + limma",
      "topics": [
        "lengthNorm.limma.createRmd"
      ]
    },
    {
      "page": "lengthNorm.sva.limma.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + SVA + limma",
      "topics": [
        "lengthNorm.sva.limma.createRmd"
      ]
    },
    {
      "page": "listcreateRmd",
      "title": "List available *.createRmd functions",
      "topics": [
        "listcreateRmd"
      ]
    },
    {
      "page": "logcpm.limma.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with limma after log-transforming the counts per million (cpm)",
      "topics": [
        "logcpm.limma.createRmd"
      ]
    },
    {
      "page": "NBPSeq.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with NBPSeq",
      "topics": [
        "NBPSeq.createRmd"
      ]
    },
    {
      "page": "NOISeq.prenorm.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with NOISeq",
      "topics": [
        "NOISeq.prenorm.createRmd"
      ]
    },
    {
      "page": "phyloCompData",
      "title": "Create a 'phyloCompData' object",
      "topics": [
        "phyloCompData"
      ]
    },
    {
      "page": "phyloCompData-class",
      "title": "Class phyloCompData",
      "topics": [
        "phyloCompData-class"
      ]
    },
    {
      "page": "phylolm.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with 'phylolm'.",
      "topics": [
        "phylolm.createRmd"
      ]
    },
    {
      "page": "runComparison",
      "title": "Run the performance comparison between differential expression methods.",
      "topics": [
        "runComparison"
      ]
    },
    {
      "page": "runComparisonGUI",
      "title": "A GUI to the main function for running the performance comparison between differential expression methods.",
      "topics": [
        "runComparisonGUI"
      ]
    },
    {
      "page": "runComparisonShiny",
      "title": "A shiny-based GUI to the main function for running the performance comparison between differential expression methods.",
      "topics": [
        "runComparisonShiny"
      ]
    },
    {
      "page": "runDiffExp",
      "title": "The main function to run differential expression analysis",
      "topics": [
        "runDiffExp"
      ]
    },
    {
      "page": "show-compData-method",
      "title": "Show method for 'compData' object",
      "topics": [
        "show,compData-method"
      ]
    },
    {
      "page": "show-phyloCompData-method",
      "title": "Show method for 'phyloCompData' object",
      "topics": [
        "show,phyloCompData-method"
      ]
    },
    {
      "page": "sqrtcpm.limma.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with limma after square root-transforming the counts per million (cpm)",
      "topics": [
        "sqrtcpm.limma.createRmd"
      ]
    },
    {
      "page": "summarizeSyntheticDataSet",
      "title": "Summarize a synthetic data set by some diagnostic plots",
      "topics": [
        "summarizeSyntheticDataSet"
      ]
    },
    {
      "page": "TCC.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with TCC",
      "topics": [
        "TCC.createRmd"
      ]
    },
    {
      "page": "ttest.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with a t-test",
      "topics": [
        "ttest.createRmd"
      ]
    },
    {
      "page": "voom.limma.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with voom+limma",
      "topics": [
        "voom.limma.createRmd"
      ]
    },
    {
      "page": "voom.ttest.createRmd",
      "title": "Generate a '.Rmd' file containing code to perform differential expression analysis with voom+t-test",
      "topics": [
        "voom.ttest.createRmd"
      ]
    }
  ],
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