{ "_id": "6a129d45acfb0bcc41d0f402", "Package": "coGPS", "Type": "Package", "Title": "cancer outlier Gene Profile Sets", "Version": "1.56.0", "Date": "2011-10-20", "Author": "Yingying Wei, Michael Ochs", "Maintainer": "Yingying Wei ", "Description": "Gene Set Enrichment Analysis of P-value based statistics\nfor outlier gene detection in dataset merged from multiple\nstudies", "License": "GPL-2", "LazyLoad": "yes", "Packaged": { "Date": "2026-05-24 06:36:05 UTC", "User": "root" }, "biocViews": "Microarray, DifferentialExpression", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:36:20 UTC", "RemoteUrl": "https://github.com/bioc/coGPS", "RemoteRef": "RELEASE_3_23", "RemoteSha": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "NeedsCompilation": "no", "MD5sum": "e2af4826d45e0297f805334e621dce0b", "_user": "bioc-release", "_type": "src", "_file": "coGPS_1.56.0.tar.gz", "_fileid": "8f60afc0c80154b1c151d68ebe52e2fa3d9b31e0000e0a565de2632db522ae61", "_filesize": 1842481, "_sha256": "8f60afc0c80154b1c151d68ebe52e2fa3d9b31e0000e0a565de2632db522ae61", "_created": "2026-05-24T06:36:05.000Z", "_published": "2026-05-24T06:40:05.089Z", "_jobs": [ { "job": 77577716747, "time": 122, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7182935029" }, { "job": 77577716762, "time": 191, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7182941785" }, { "job": 77577716743, "time": 206, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7182943159" }, { "job": 77577716753, "time": 70, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7182930128" }, { "job": 77577716759, "time": 120, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7182934826" }, { "job": 77577577328, "time": 174, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7182923357" }, { "job": 77577716745, "time": 80, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7182931039" }, { "job": 77577716754, "time": 88, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7182931860" }, { "job": 77577716761, "time": 57, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7182929084" }, { "job": 77577716756, "time": 69, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7182930073" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/coGPS", "_commit": { "id": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "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": 1777379780 }, "_maintainer": { "name": "Yingying Wei", "email": "ywei@jhsph.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "limma", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.57.0", "bioc": "3.24" }, { "branch": "release", "version": "1.56.0", "bioc": "3.23" } ], "_topics": [ "microarray", "differentialexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 441, "source": "https://www.bioconductor.org/packages/stats/bioc/coGPS" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/coGPS.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "PatientSpecificGeneList", "PCOPA", "permCOPA", "plotCOPA", "PlotTopPCOPA" ], "_datasets": [ { "name": "CNV_classlab_matched", "title": "Sample Data for coGPS", "object": "CNV_classlab_matched", "file": "CNV_classlab_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "x" ], "rows": 69, "table": true, "tojson": true }, { "name": "CNV_exprs_matched", "title": "Sample Data for coGPS", "object": "CNV_exprs_matched", "file": "CNV_exprs_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22", "X23", "X24", "X25", "X26", "X28", "X29", "X30", "X31", "X32", "X34", "X36", "X37", "X39", "X40", "X42", "X43", "X44", "X45", "X46", "X48", "X49", "X50", "X101", "X102", "X103", "X104", "X105", "X106", "X107", "X108", "X109", "X110", "X111", "X112", "X113", "X114", "X115", "X116", "X117", "X118", "X119", "X120", "X121", "X122", "X123", "X124", "X125" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Exon_classlab_matched", "title": "Sample Data for coGPS", "object": "Exon_classlab_matched", "file": "Exon_classlab_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "x" ], "rows": 69, "table": true, "tojson": true }, { "name": "Exon_exprs_matched", "title": "Sample Data for coGPS", "object": "Exon_exprs_matched", "file": "Exon_exprs_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22", "X23", "X24", "X25", "X26", "X28", "X29", "X30", "X31", "X32", "X34", "X36", "X37", "X39", "X40", "X42", "X43", "X44", "X45", "X46", "X48", "X49", "X50", "X101", "X102", "X103", "X104", "X105", "X106", "X107", "X108", "X109", "X110", "X111", "X112", "X113", "X114", "X115", "X116", "X117", "X118", "X119", "X120", "X121", "X122", "X123", "X124", "X125" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Hs.gmtl.c1", "title": "Sample Data for coGPS", "object": "human_c1", "file": "human_c1.rdata", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "Methy_classlab_matched", "title": "Sample Data for coGPS", "object": "Methy_classlab_matched", "file": "Methy_classlab_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "x" ], "rows": 69, "table": true, "tojson": true }, { "name": "Methy_exprs_matched", "title": "Sample Data for coGPS", "object": "Methy_exprs_matched", "file": "Methy_exprs_matched.txt.gz", "class": [ "data.frame" ], "fields": [ "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22", "X23", "X24", "X25", "X26", "X28", "X29", "X30", "X31", "X32", "X34", "X36", "X37", "X39", "X40", "X42", "X43", "X44", "X45", "X46", "X48", "X49", "X50", "X101", "X102", "X103", "X104", "X105", "X106", "X107", "X108", "X109", "X110", "X111", "X112", "X113", "X114", "X115", "X116", "X117", "X118", "X119", "X120", "X121", "X122", "X123", "X124", "X125" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "coGPS-package", "title": "Cancer Outlier Gene Profile Sets", "topics": [ "coGPS-package", "coGPS" ] }, { "page": "coGPS-internal", "title": "coGPS package internal function.", "topics": [ "plotCOPA" ] }, { "page": "PatientSpecificGeneList", "title": "Patient Specific outlier gene list", "topics": [ "PatientSpecificGeneList" ] }, { "page": "PCOPA", "title": "P-value based outlier gene detection", "topics": [ "PCOPA" ] }, { "page": "permCOPA", "title": "Calculate PCOPA value for permuations", "topics": [ "permCOPA" ] }, { "page": "PlotTopPCOPA", "title": "Plot expression patterns of top ranked genes.", "topics": [ "PlotTopPCOPA" ] }, { "page": "SampleData", "title": "Sample Data for coGPS", "topics": [ "CNV_classlab_matched", "CNV_exprs_matched", "Exon_classlab_matched", "Exon_exprs_matched", "Hs.gmtl.c1", "Methy_classlab_matched", "Methy_exprs_matched" ] } ], "_rundeps": [], "_vignettes": [ { "source": "coGPS.Rnw", "filename": "coGPS.pdf", "title": "coGPS", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:24:10", "modified": "2013-11-01 20:24:10", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "cogps", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/coGPS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.56.0", "date": "2026-05-24T06:39:13.000Z", "distro": "noble", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "bbd89f12e7170aa34cbb286081450ecdeb47bfced9ab6b708ce490bb6e752382", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.6.0", "os": "linux", "version": "1.56.0", "date": "2026-05-24T06:39:31.000Z", "distro": "noble", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "855ed447198b101fb74a2a7584cdd9cdb3666203b4bcf3859499317f37a21a5e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.5.3", "os": "mac", "version": "1.56.0", "date": "2026-05-24T06:37:22.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "8ed8ded52eba37cc2f533e6eec4da794326070b75688024b025ada4fa55d590a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.6.0", "os": "mac", "version": "1.56.0", "date": "2026-05-24T06:38:04.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "a6b682fb2c0d647a382382dd7cc63e41f57667c7ebe68ba1f44962ac34af8733", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.6.0", "os": "wasm", "version": "1.56.0", "date": "2026-05-24T06:37:40.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "270b4effac665ca20966fafd86a65c75d6d3b156ff1a1b3006ee6d92badd4e65", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.7.0", "os": "win", "version": "1.56.0", "date": "2026-05-24T06:37:28.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "73ea3c16e5581120b6b7ca068c870cb1d82df8727ce934de6d0d6b1c8f9dfbe4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.5.3", "os": "win", "version": "1.56.0", "date": "2026-05-24T06:36:59.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "b4dd152e8310ad6b6f311814c3be442bcd65ed9db487cccebc59e3837d0b1727", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" }, { "r": "4.6.0", "os": "win", "version": "1.56.0", "date": "2026-05-24T06:37:08.000Z", "commit": "53b7004e799ec5eae78d9e8f1f044fd3b688744b", "fileid": "8cab1fe931110f0c2faa1e748ccecc307dbb8d1eb38a51f3b604be29d9f3936c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354104367" } ] }