{ "_id": "6a290b31732311cd875942a2", "Package": "copa", "Title": "Functions to perform cancer outlier profile analysis.", "Version": "1.80.0", "Date": "2006-01-26", "Author": "James W. MacDonald", "Maintainer": "James W. MacDonald ", "Description": "COPA is a method to find genes that undergo recurrent\nfusion in a given cancer type by finding pairs of genes that\nhave mutually exclusive outlier profiles.", "License": "Artistic-2.0", "LazyLoad": "yes", "biocViews": "OneChannel, TwoChannel, DifferentialExpression,\nVisualization", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:31:38 UTC", "RemoteUrl": "https://github.com/bioc/copa", "RemoteRef": "RELEASE_3_23", "RemoteSha": "606f635a075f10c74bcd95d88012386a4a36a30b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-10 06:52:41 UTC", "User": "root" }, "MD5sum": "7fbf5f48fc2fae2caf8a18c1f2b50b9d", "_user": "bioc-release", "_type": "src", "_file": "copa_1.80.0.tar.gz", "_fileid": "f6ae5c5461531ea4ccc850b258016a168ecde58febf2b1027da5c19a1f2fefb7", "_filesize": 228742, "_sha256": "f6ae5c5461531ea4ccc850b258016a168ecde58febf2b1027da5c19a1f2fefb7", "_created": "2026-06-10T06:52:41.000Z", "_published": "2026-06-10T06:58:57.261Z", "_jobs": [ { "job": 80499184091, "time": 124, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7528572212" }, { "job": 80499184174, "time": 104, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7528567530" }, { "job": 80499184149, "time": 133, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7528574675" }, { "job": 80499184116, "time": 112, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7528569739" }, { "job": 80499184142, "time": 121, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7528571509" }, { "job": 80499184120, "time": 105, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7528567003" }, { "job": 80499184107, "time": 158, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7528581738" }, { "job": 80499184140, "time": 119, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7528570664" }, { "job": 80499184125, "time": 346, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7528635269" }, { "job": 80498822908, "time": 149, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7528536944" }, { "job": 80499184106, "time": 89, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7528562429" }, { "job": 80499184100, "time": 118, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7528570429" }, { "job": 80499184115, "time": 75, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7528558602" }, { "job": 80499184148, "time": 74, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7528558162" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/copa", "_commit": { "id": "606f635a075f10c74bcd95d88012386a4a36a30b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379498 }, "_maintainer": { "name": "James W. MacDonald", "email": "jmacdon@u.washington.edu", "login": "jmacdon", "description": "", "uuid": 5940924 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Biobase", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "colonCA", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.81.0", "bioc": "3.24" }, { "branch": "release", "version": "1.80.0", "bioc": "3.23" } ], "_topics": [ "onechannel", "twochannel", "differentialexpression", "visualization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 470, "source": "https://www.bioconductor.org/packages/stats/bioc/copa" }, "_mentions": 2, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/copa.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "copa", "copaPerm", "plotCopa", "scatterPlotCopa", "summaryCopa", "tableCopa" ], "_help": [ { "page": "copa.package", "title": "copa - A package to compute 'Cancer Outlier Profile Analysis'", "topics": [ "copa-package" ] }, { "page": "copa", "title": "Calculate COPA Scores from a Set of Microarrays", "topics": [ "copa" ] }, { "page": "copaPerm", "title": "Measure Significance of COPA by Permutation", "topics": [ "copaPerm" ] }, { "page": "plotCopa", "title": "Plot Gene Pairs fom the Results of Running copa", "topics": [ "plotCopa" ] }, { "page": "scatterPlotCopa", "title": "Create scatterplots of interesting gene pairs", "topics": [ "scatterPlotCopa" ] }, { "page": "summaryCopa", "title": "Create Summary Showing Top Gene Pairs", "topics": [ "summaryCopa" ] }, { "page": "copaTable", "title": "Summarize copa results", "topics": [ "tableCopa" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics" ], "_vignettes": [ { "source": "copa.Rnw", "filename": "copa.pdf", "title": "copa Overview", "engine": "utils::Sweave", "headings": [ "Overview", "Introduction", "Using copa" ], "created": "2013-10-21 17:08:50", "modified": "2013-10-21 17:08:50", "commits": 1 } ], "_score": 3.6020599913279625, "_indexed": false, "_nocasepkg": "copa", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/copa", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.80.0", "date": "2026-06-10T06:54:32.000Z", "distro": "noble", "arch": "aarch64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "7168064d83c601357b17826c34c66b5e3da83d073973e97abd11f9334e1f2b70", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.7.0", "os": "linux", "version": "1.80.0", "date": "2026-06-10T06:54:52.000Z", "distro": "noble", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "1c7e9c2d074c15a3c7d6f61c42a0d84d019138248d819ea4158fc3cb237ec706", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "linux", "version": "1.80.0", "date": "2026-06-10T06:54:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "1abcdd50943a156c577f009cb91cb79378a1edfd6e5ab362e9baec6fd235df6d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "linux", "version": "1.80.0", "date": "2026-06-10T06:54:43.000Z", "distro": "noble", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "fdef6ea3a1e0bb7c107e3e0d4174af5cd887e60e6e786f0b3f703a9c3342d24b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.5.3", "os": "mac", "version": "1.80.0", "date": "2026-06-10T06:54:22.000Z", "arch": "aarch64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "564ac09973c88e31513126d8e2fec8051bd7dcd453683665b738d1707ed369c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.5.3", "os": "mac", "version": "1.80.0", "date": "2026-06-10T06:55:11.000Z", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "74ae75ac105aa7bd7271f16b4f30a28de3316c9792234e073ed2ca7aff24d70f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "mac", "version": "1.80.0", "date": "2026-06-10T06:54:30.000Z", "arch": "aarch64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "13285212c6fda5bb751588926bcdb775b14c82857495d28c23498ca8d1fd93e1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "mac", "version": "1.80.0", "date": "2026-06-10T06:57:57.000Z", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "e3ddfee200117bce028837c787bdd39d7869d0bcdb1765420be6b26155036fe3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "wasm", "version": "1.80.0", "date": "2026-06-10T06:54:23.000Z", "arch": "emscripten", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "161c2dfe5e06da154e83fa90c6c6bdb55f9dae274bddab95f494b6e59f6f667f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.7.0", "os": "win", "version": "1.80.0", "date": "2026-06-10T06:54:30.000Z", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "5f9994c3e0ae2dbb3a71c9f8812135a08427cbd272cf2e254d52c2e1f7d2c7ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.5.3", "os": "win", "version": "1.80.0", "date": "2026-06-10T06:53:46.000Z", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "d2bcaa928615a521a8d30c5a047c5cdd6b875ca3299dbd10844e4aa56348c50b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" }, { "r": "4.6.0", "os": "win", "version": "1.80.0", "date": "2026-06-10T06:53:41.000Z", "arch": "x86_64", "commit": "606f635a075f10c74bcd95d88012386a4a36a30b", "fileid": "213da5976da067be4f543c67704bdcd42b16bc1a54ffd53b4b7f667dd154061f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27258648907" } ] }