{ "_id": "6a101a0aacfb0bcc41c863a0", "Package": "iCOBRA", "Type": "Package", "Title": "Comparison and Visualization of Ranking and Assignment Methods", "Version": "1.41.1", "Date": "2026-05-10", "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", "URL": "https://csoneson.github.io/iCOBRA/", "BugReports": "https://github.com/csoneson/iCOBRA/issues", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-14 06:29:43 UTC", "RemoteUrl": "https://github.com/bioc/iCOBRA", "RemoteRef": "HEAD", "RemoteSha": "88db64687355e49d27c434c3da078ede61508dcd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 10:15:54 UTC", "User": "root" }, "Author": "Charlotte Soneson [aut, cre] (ORCID:\n)", "Maintainer": "Charlotte Soneson ", "MD5sum": "fae0d26d4223e71270e0dfea0bcbf639", "_user": "bioc", "_type": "src", "_file": "iCOBRA_1.41.1.tar.gz", "_fileid": "cf4a2aeab577273d868f13b8f2c92bccf22b81ad09b95ee171546dc3ec5887fb", "_filesize": 3936341, "_sha256": "cf4a2aeab577273d868f13b8f2c92bccf22b81ad09b95ee171546dc3ec5887fb", "_created": "2026-05-14T10:15:54.000Z", "_published": "2026-05-22T08:55:38.249Z", "_jobs": [ { "job": 77347697901, "time": 172, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "6992167137" }, { "job": 77347697998, "time": 207, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6992176620" }, { "job": 77347697617, "time": 385, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6992225799" }, { "job": 77347697997, "time": 176, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6992168208" }, { "job": 77347697971, "time": 172, "config": "macos-release-arm64", "r": 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"message": "Merge pull request #8 from csoneson/simpleupset\n\nSwitch to SimpleUpset", "time": 1778740183 }, "_maintainer": { "name": "Charlotte Soneson", "email": "charlottesoneson@gmail.com", "login": "csoneson", "orcid": "0000-0003-3833-2169", "uuid": 5628952 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "shiny", "version": ">= 0.9.1.9008", "role": "Imports" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "ROCR", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "prompter", "role": 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"_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": [ "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": [ "prepare_data_for_plot" ] }, { "page": "pval", "title": "Accessor and replacement functions for 'pval' slot", "topics": [ "pval", "pval,COBRAData-method", "pval<-", "pval<-,COBRAData,data.frame-method" ] }, { "page": "reorder_levels", "title": "Reorder levels in COBRAPlot object", "topics": [ "reorder_levels" ] }, { "page": "roc", "title": "Accessor and replacement functions for 'roc' slot", "topics": [ "roc", "roc,COBRAPerformance-method", "roc,COBRAPlot-method", "roc<-", "roc<-,COBRAPerformance,data.frame-method", "roc<-,COBRAPlot,data.frame-method" ] }, { "page": "scatter", "title": "Accessor and replacement functions for 'scatter' slot", "topics": [ "scatter", "scatter,COBRAPerformance-method", "scatter,COBRAPlot-method", "scatter<-", "scatter<-,COBRAPerformance,data.frame-method", "scatter<-,COBRAPlot,data.frame-method" ] }, { "page": "score", "title": "Accessor and replacement functions for 'score' slot", "topics": [ "score", "score,COBRAData-method", "score<-", "score<-,COBRAData,data.frame-method" ] }, { "page": "splv", "title": "Accessor and replacement functions for 'splv' slot", "topics": [ "splv", "splv,COBRAPerformance-method", "splv,COBRAPlot-method", "splv<-", "splv<-,COBRAPerformance,character-method", "splv<-,COBRAPlot,character-method" ] }, { "page": "stratiflevels", "title": "Accessor function for stratification levels", "topics": [ "stratiflevels", "stratiflevels,COBRAPerformance-method", "stratiflevels,COBRAPlot-method" ] }, { "page": "sval", "title": "Accessor and replacement functions for 'sval' slot", "topics": [ "sval", "sval,COBRAData-method", "sval<-", "sval<-,COBRAData,data.frame-method" ] }, { "page": "tpr", "title": "Accessor and replacement functions for 'tpr' slot", "topics": [ "tpr", "tpr,COBRAPerformance-method", "tpr,COBRAPlot-method", "tpr<-", "tpr<-,COBRAPerformance,data.frame-method", "tpr<-,COBRAPlot,data.frame-method" ] }, { "page": "truth", "title": "Accessor and replacement functions for 'truth' slot", "topics": [ "truth", "truth,COBRAData-method", "truth<-", 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