{
  "_id": "6ae7522b9ceaa78f20099d0e",
  "Package": "ReportingTools",
  "Title": "Tools for making reports in various formats",
  "Version": "2.53.0",
  "Author": "Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina\nChaivorapol, Gabriel Becker, and Josh Kaminker",
  "Maintainer": "Jason A. Hackney <hackney.jason@gene.com>, Gabriel Becker\n<becker.gabe@gene.com>, Jessica L. Larson\n<larson.jessica@gmail.com>",
  "Type": "Package",
  "LazyLoad": "yes",
  "License": "Artistic-2.0",
  "Description": "The ReportingTools software package enables users to\neasily display reports of analysis results generated from\nsources such as microarray and sequencing data.  The package\nallows users to create HTML pages that may be viewed on a web\nbrowser such as Safari, or in other formats readable by\nprograms such as Excel.  Users can generate tables with\nsortable and filterable columns, make and display plots, and\nlink table entries to other data sources such as NCBI or larger\nplots within the HTML page.  Using the package, users can also\nproduce a table of contents page to link various reports\ntogether for a particular project that can be viewed in a web\nbrowser.  For more examples, please visit our site: http://\nresearch-pub.gene.com/ReportingTools.",
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  "biocViews": "ImmunoOncology, Software, Visualization, Microarray, RNASeq,\nGO, DataRepresentation, GeneSetEnrichment",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:54 UTC",
  "RemoteUrl": "https://github.com/bioc/ReportingTools",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 13:17:06 UTC",
    "User": "root"
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  "_type": "src",
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  "_expires": "2027-02-09T14:52:25.000Z",
  "_created": "2026-11-01T13:17:06.000Z",
  "_published": "2026-11-01T14:52:27.163Z",
  "_upstream": "https://github.com/bioc/ReportingTools",
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  "_maintainer": {
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    "email": "hackney.jason@gene.com",
    "login": "jasonhackney",
    "description": "Computational biologist focusing on drug discovery and development",
    "uuid": 31082488
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        "filename-methods"
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        "finish-methods"
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        "basePath,HTMLReport-method",
        "baseUrl",
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        "path,HTMLReportRef-method",
        "publish,ANY,HTMLReportRef-method",
        "show,HTMLReportRef-method",
        "[[,HTMLReportRef,ANY,ANY-method",
        "[[,HTMLReportRef,ANY-method",
        "[[<-,HTMLReportRef,ANY,ANY,ANY-method"
      ]
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    {
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        "Link,character-method",
        "Link,HTMLReportRef-method",
        "Link,list-method",
        "Link-methods"
      ]
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      "topics": [
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      "topics": [
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      "page": "addReportColumns-methods",
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      "topics": [
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        "modifyReportDF,ANY,ANY,ANY-method",
        "modifyReportDF,ANY,ANY,DESeqDataSet-method",
        "modifyReportDF,ANY,ANY,DESeqResults-method",
        "modifyReportDF,ANY,ANY,DGEExact-method",
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        "modifyReportDF,ANY,ANY,GeneSet-method",
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        "objectToHTML,ANY-method",
        "objectToHTML,character-method",
        "objectToHTML,data.frame-method",
        "objectToHTML,ggbio-method",
        "objectToHTML,ggplot-method",
        "objectToHTML,recordedplot-method",
        "objectToHTML,trellis-method",
        "objectToHTML,XMLInternalNode-method",
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        "publish,character,DataPackage-method",
        "publish,data.frame,CSVFile-method",
        "publish,data.frame,DataPackage-method",
        "publish,data.frame,HTMLReport-method",
        "publish,data.frame,HTMLReportRef-method",
        "publish,DESeqDataSet,HTMLReportRef-method",
        "publish,DESeqResults,HTMLReportRef-method",
        "publish,DGEExact,ANY-method",
        "publish,DGEExact,HTMLReport-method",
        "publish,DGEExact,HTMLReportRef-method",
        "publish,DGELRT,ANY-method",
        "publish,DGELRT,HTMLReport-method",
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        "publish,GeneSet,HTMLReport-method",
        "publish,GeneSetCollection,ANY-method",
        "publish,GeneSetCollection,HTMLReport-method",
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        "publish,GOHyperGResult,ANY-method",
        "publish,GOHyperGResult,HTMLReport-method",
        "publish,GOHyperGResult,HTMLReportRef-method",
        "publish,HTMLReport,HTMLReport-method",
        "publish,HTMLReport,HTMLReportRef-method",
        "publish,HyperGResultBase,HTMLReport-method",
        "publish,HyperGResultBase,HTMLReportRef-method",
        "publish,list,HTMLReport-method",
        "publish,list,HTMLReportRef-method",
        "publish,MArrayLM,ANY-method",
        "publish,MArrayLM,HTMLReport-method",
        "publish,MArrayLM,HTMLReportRef-method",
        "publish,PFAMHyperGResult,ANY-method",
        "publish,PFAMHyperGResult,HTMLReport-method",
        "publish,PFAMHyperGResult,HTMLReportRef-method",
        "publish,trellis,HTMLReport-method",
        "publish,trellis,HTMLReportRef-method",
        "publish-methods"
      ]
    },
    {
      "page": "readReport",
      "title": "Read in an Existing Report",
      "topics": [
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      ]
    },
    {
      "page": "ReportHandlers-class",
      "title": "Class '\"ReportHandlers\"'",
      "topics": [
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        "fileHandlers",
        "fileWIndexHandlers",
        "knitrHandlers",
        "path,ReportHandlers-method",
        "ReportHandlers-class",
        "shinyHandlers"
      ]
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      "title": "Color theme for use in ReportingTools",
      "topics": [
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      ]
    },
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      "title": "Alternate color theme for use in ReportingTools",
      "topics": [
        "reporting.theme.alternate"
      ]
    },
    {
      "page": "toReportDF-methods",
      "title": "Class Specific Default Behavior for Transforming Objects to data.frames",
      "topics": [
        "toReportDF",
        "toReportDF,ANY-method",
        "toReportDF,data.frame-method",
        "toReportDF,DESeqDataSet-method",
        "toReportDF,DESeqResults-method",
        "toReportDF,DGEExact-method",
        "toReportDF,DGELRT-method",
        "toReportDF,GeneSet-method",
        "toReportDF,GeneSetCollection-method",
        "toReportDF,GOHyperGResult-method",
        "toReportDF,MArrayLM-method",
        "toReportDF,PFAMHyperGResult-method",
        "toReportDF-methods"
      ]
    },
    {
      "page": "validConnection",
      "title": "Determine connection validity",
      "topics": [
        "validConnection"
      ]
    }
  ],
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