{
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  "Package": "iCOBRA",
  "Type": "Package",
  "Title": "Comparison and Visualization of Ranking and Assignment Methods",
  "Version": "1.40.0",
  "Date": "2025-12-13",
  "Authors@R": "c(person(given = \"Charlotte\", family = \"Soneson\", \nrole = c(\"aut\", \"cre\"),\nemail = \"charlottesoneson@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3833-2169\")))",
  "Description": "This package provides functions for calculation and\nvisualization of performance metrics for evaluation of ranking\nand binary classification (assignment) methods. Various types\nof performance plots can be generated programmatically. The\npackage also contains a shiny application for interactive\nexploration of results.",
  "License": "GPL (>=2)",
  "Collate": "'AllGenerics.R' 'COBRAData.R' 'COBRAPerformance.R'\n'COBRAPlot.R' 'calculate_performance.R' 'cobradata_example.R'\n'cobradata_example_sval.R' 'helpers_general.R' 'plot_methods.R'\n'printHead.R' 'shiny.R'",
  "VignetteBuilder": "knitr",
  "biocViews": "Classification, Visualization",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "URL": "https://csoneson.github.io/iCOBRA/",
  "BugReports": "https://github.com/csoneson/iCOBRA/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:14 UTC",
  "RemoteUrl": "https://github.com/bioc/iCOBRA",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "b16914708d58c5a905baf6c80e431030f754273a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-17 07:34:09 UTC",
    "User": "root"
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  "Author": "Charlotte Soneson [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3833-2169>)",
  "Maintainer": "Charlotte Soneson <charlottesoneson@gmail.com>",
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  "_created": "2026-06-17T07:34:09.000Z",
  "_published": "2026-06-17T07:40:25.959Z",
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      "package": "shinydashboard",
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      "package": "prompter",
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      "package": "markdown",
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    {
      "package": "rmarkdown",
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      "package": "testthat",
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  "_selfowned": false,
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  "_updates": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_mentions": 5,
  "_devurl": "https://github.com/csoneson/icobra",
  "_pkgdown": "https://csoneson.github.io/iCOBRA/",
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  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/iCOBRA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/csoneson/icobra",
  "_realowner": "bioc",
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  "_exports": [
    ".COBRAData",
    ".COBRAPerformance",
    ".COBRAPlot",
    "basemethods",
    "calculate_adjp",
    "calculate_performance",
    "COBRAapp",
    "COBRAData",
    "COBRAData_from_text",
    "COBRAData_to_text",
    "COBRAPerformance",
    "COBRAPlot",
    "coerce",
    "corr",
    "corr<-",
    "deviation",
    "deviation<-",
    "facetted",
    "facetted<-",
    "fdrnbr",
    "fdrnbr<-",
    "fdrnbrcurve",
    "fdrnbrcurve<-",
    "fdrtpr",
    "fdrtpr<-",
    "fdrtprcurve",
    "fdrtprcurve<-",
    "fpc",
    "fpc<-",
    "fpr",
    "fpr<-",
    "fsrnbr",
    "fsrnbr<-",
    "fsrnbrcurve",
    "fsrnbrcurve<-",
    "maxsplit",
    "maxsplit<-",
    "onlyshared",
    "onlyshared<-",
    "overlap",
    "overlap<-",
    "padj",
    "padj<-",
    "plot_corr",
    "plot_deviation",
    "plot_fdrnbrcurve",
    "plot_fdrtprcurve",
    "plot_fpc",
    "plot_fpr",
    "plot_fsrnbrcurve",
    "plot_overlap",
    "plot_roc",
    "plot_scatter",
    "plot_tpr",
    "plot_upset",
    "plotcolors",
    "plotcolors<-",
    "prepare_data_for_plot",
    "pval",
    "pval<-",
    "reorder_levels",
    "roc",
    "roc<-",
    "scatter",
    "scatter<-",
    "score",
    "score<-",
    "splv",
    "splv<-",
    "stratiflevels",
    "sval",
    "sval<-",
    "tpr",
    "tpr<-",
    "truth",
    "truth<-",
    "update_cobradata",
    "update_cobraperformance"
  ],
  "_datasets": [
    {
      "name": "cobradata_example",
      "title": "Example data set with three differential gene expression methods",
      "object": "cobradata_example",
      "file": "cobradata_example.rda",
      "class": [
        "COBRAData"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cobradata_example_sval",
      "title": "Example data set with three differential gene expression methods",
      "object": "cobradata_example_sval",
      "file": "cobradata_example_sval.rda",
      "class": [
        "COBRAData"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "basemethods",
      "title": "Accessor function for basemethods",
      "topics": [
        "basemethods",
        "basemethods,COBRAPerformance-method",
        "basemethods,COBRAPlot-method"
      ]
    },
    {
      "page": "calculate_adjp",
      "title": "Calculate adjusted p-values",
      "topics": [
        "calculate_adjp"
      ]
    },
    {
      "page": "calculate_performance",
      "title": "Calculate performance measures",
      "topics": [
        "calculate_performance"
      ]
    },
    {
      "page": "COBRAapp",
      "title": "Interactive shiny app to visualize results",
      "topics": [
        "COBRAapp"
      ]
    },
    {
      "page": "cobradata_example",
      "title": "Example data set with three differential gene expression methods",
      "topics": [
        "cobradata_example"
      ]
    },
    {
      "page": "cobradata_example_sval",
      "title": "Example data set with three differential gene expression methods",
      "topics": [
        "cobradata_example_sval"
      ]
    },
    {
      "page": "COBRAData",
      "title": "'COBRAData' object and constructor",
      "topics": [
        ".COBRAData",
        "COBRAData",
        "COBRAData-class",
        "COBRAData_from_text",
        "COBRAData_to_text"
      ]
    },
    {
      "page": "COBRAPerformance",
      "title": "'COBRAPerformance' object and constructor",
      "topics": [
        ".COBRAPerformance",
        "COBRAPerformance",
        "COBRAPerformance-class"
      ]
    },
    {
      "page": "COBRAPlot",
      "title": "'COBRAPlot' object and constructor",
      "topics": [
        ".COBRAPlot",
        "COBRAPlot",
        "COBRAPlot-class"
      ]
    },
    {
      "page": "coerce",
      "title": "Convert an object to another class",
      "topics": [
        "COBRAPlot,COBRAPerformance-method",
        "coerce",
        "coerce,",
        "coerce,COBRAPerformance,COBRAPlot-method",
        "coerce,COBRAPlot,COBRAPerformance-method"
      ]
    },
    {
      "page": "corr",
      "title": "Accessor and replacement functions for 'corr' slot",
      "topics": [
        "corr",
        "corr,COBRAPerformance-method",
        "corr,COBRAPlot-method",
        "corr<-",
        "corr<-,COBRAPerformance,data.frame-method",
        "corr<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "deviation",
      "title": "Accessor and replacement functions for 'deviation' slot",
      "topics": [
        "deviation",
        "deviation,COBRAPerformance-method",
        "deviation,COBRAPlot-method",
        "deviation<-",
        "deviation<-,COBRAPerformance,data.frame-method",
        "deviation<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "Extract",
      "title": "Subsetting 'COBRAData', 'COBRAPerformance' or 'COBRAPlot' objects",
      "topics": [
        "Extract",
        "[",
        "[,COBRAData-method",
        "[,COBRAPerformance-method",
        "[,COBRAPlot-method",
        "\\S4method{[}{COBRAData,ANY,ANY,ANY}",
        "\\S4method{[}{COBRAData,ANY,ANY}",
        "\\S4method{[}{COBRAPerformance,ANY,ANY,ANY}",
        "\\S4method{[}{COBRAPerformance,ANY,ANY}",
        "\\S4method{[}{COBRAPlot,ANY,ANY,ANY}",
        "\\S4method{[}{COBRAPlot,ANY,ANY}"
      ]
    },
    {
      "page": "facetted",
      "title": "Accessor and replacement functions for 'facetted' slot",
      "topics": [
        "facetted",
        "facetted,COBRAPlot-method",
        "facetted<-",
        "facetted<-,COBRAPlot,logical-method"
      ]
    },
    {
      "page": "fdrnbr",
      "title": "Accessor and replacement functions for 'fdrnbr' slot",
      "topics": [
        "fdrnbr",
        "fdrnbr,COBRAPerformance-method",
        "fdrnbr,COBRAPlot-method",
        "fdrnbr<-",
        "fdrnbr<-,COBRAPerformance,data.frame-method",
        "fdrnbr<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fdrnbrcurve",
      "title": "Accessor and replacement functions for 'fdrnbrcurve' slot",
      "topics": [
        "fdrnbrcurve",
        "fdrnbrcurve,COBRAPerformance-method",
        "fdrnbrcurve,COBRAPlot-method",
        "fdrnbrcurve<-",
        "fdrnbrcurve<-,COBRAPerformance,data.frame-method",
        "fdrnbrcurve<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fdrtpr",
      "title": "Accessor and replacement functions for 'fdrtpr' slot",
      "topics": [
        "fdrtpr",
        "fdrtpr,COBRAPerformance-method",
        "fdrtpr,COBRAPlot-method",
        "fdrtpr<-",
        "fdrtpr<-,COBRAPerformance,data.frame-method",
        "fdrtpr<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fdrtprcurve",
      "title": "Accessor and replacement functions for 'fdrtprcurve' slot",
      "topics": [
        "fdrtprcurve",
        "fdrtprcurve,COBRAPerformance-method",
        "fdrtprcurve,COBRAPlot-method",
        "fdrtprcurve<-",
        "fdrtprcurve<-,COBRAPerformance,data.frame-method",
        "fdrtprcurve<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fpc",
      "title": "Accessor and replacement functions for 'fpc' slot",
      "topics": [
        "fpc",
        "fpc,COBRAPerformance-method",
        "fpc,COBRAPlot-method",
        "fpc<-",
        "fpc<-,COBRAPerformance,data.frame-method",
        "fpc<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fpr",
      "title": "Accessor and replacement functions for 'fpr' slot",
      "topics": [
        "fpr",
        "fpr,COBRAPerformance-method",
        "fpr,COBRAPlot-method",
        "fpr<-",
        "fpr<-,COBRAPerformance,data.frame-method",
        "fpr<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fsrnbr",
      "title": "Accessor and replacement functions for 'fsrnbr' slot",
      "topics": [
        "fsrnbr",
        "fsrnbr,COBRAPerformance-method",
        "fsrnbr,COBRAPlot-method",
        "fsrnbr<-",
        "fsrnbr<-,COBRAPerformance,data.frame-method",
        "fsrnbr<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "fsrnbrcurve",
      "title": "Accessor and replacement functions for 'fsrnbrcurve' slot",
      "topics": [
        "fsrnbrcurve",
        "fsrnbrcurve,COBRAPerformance-method",
        "fsrnbrcurve,COBRAPlot-method",
        "fsrnbrcurve<-",
        "fsrnbrcurve<-,COBRAPerformance,data.frame-method",
        "fsrnbrcurve<-,COBRAPlot,data.frame-method"
      ]
    },
    {
      "page": "maxsplit",
      "title": "Accessor and replacement functions for 'maxsplit' slot",
      "topics": [
        "maxsplit",
        "maxsplit,COBRAPerformance-method",
        "maxsplit,COBRAPlot-method",
        "maxsplit<-",
        "maxsplit<-,COBRAPerformance,numeric-method",
        "maxsplit<-,COBRAPlot,numeric-method"
      ]
    },
    {
      "page": "onlyshared",
      "title": "Accessor and replacement functions for 'onlyshared' slot",
      "topics": [
        "onlyshared",
        "onlyshared,COBRAPerformance-method",
        "onlyshared,COBRAPlot-method",
        "onlyshared<-",
        "onlyshared<-,COBRAPerformance,logical-method",
        "onlyshared<-,COBRAPlot,logical-method"
      ]
    },
    {
      "page": "overlap",
      "title": "Accessor and replacement functions for 'overlap' slot",
      "topics": [
        "overlap",
        "overlap,COBRAPerformance-method",
        "overlap,COBRAPlot-method",
        "overlap<-",
        "overlap<-,COBRAPerformance,list_df-method",
        "overlap<-,COBRAPlot,list_df-method"
      ]
    },
    {
      "page": "padj",
      "title": "Accessor and replacement functions for 'padj' slot",
      "topics": [
        "padj",
        "padj,COBRAData-method",
        "padj<-",
        "padj<-,COBRAData,data.frame-method"
      ]
    },
    {
      "page": "plot_corr",
      "title": "Plot correlations",
      "topics": [
        "plot_corr"
      ]
    },
    {
      "page": "plot_deviation",
      "title": "Plot deviations",
      "topics": [
        "plot_deviation"
      ]
    },
    {
      "page": "plot_fdrnbrcurve",
      "title": "Plot number of significant features vs FDR",
      "topics": [
        "plot_fdrnbrcurve"
      ]
    },
    {
      "page": "plot_fdrtprcurve",
      "title": "Plot TPR vs FDR",
      "topics": [
        "plot_fdrtprcurve"
      ]
    },
    {
      "page": "plot_fpc",
      "title": "Plot FP curves",
      "topics": [
        "plot_fpc"
      ]
    },
    {
      "page": "plot_fpr",
      "title": "Plot FPR",
      "topics": [
        "plot_fpr"
      ]
    },
    {
      "page": "plot_fsrnbrcurve",
      "title": "Plot number of features with s-value below threshold vs FSR",
      "topics": [
        "plot_fsrnbrcurve"
      ]
    },
    {
      "page": "plot_overlap",
      "title": "Plot Venn diagram",
      "topics": [
        "plot_overlap"
      ]
    },
    {
      "page": "plot_roc",
      "title": "Plot ROC curves",
      "topics": [
        "plot_roc"
      ]
    },
    {
      "page": "plot_scatter",
      "title": "Plot scatter plots",
      "topics": [
        "plot_scatter"
      ]
    },
    {
      "page": "plot_tpr",
      "title": "Plot TPR",
      "topics": [
        "plot_tpr"
      ]
    },
    {
      "page": "plot_upset",
      "title": "Create UpSet plots",
      "topics": [
        "plot_upset"
      ]
    },
    {
      "page": "plotcolors",
      "title": "Accessor and replacement functions for 'plotcolors' slot",
      "topics": [
        "plotcolors",
        "plotcolors,COBRAPlot-method",
        "plotcolors<-",
        "plotcolors<-,COBRAPlot,character-method"
      ]
    },
    {
      "page": "prepare_data_for_plot",
      "title": "Prepare data for plotting",
      "topics": [
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