{ "_id": "6a1afb1c1d7bb097a09fcadc", "Package": "RTopper", "Type": "Package", "Title": "This package is designed to perform Gene Set Analysis across\nmultiple genomic platforms", "Version": "1.58.0", "Date": "2011-09-14", "Author": "Luigi Marchionni , Svitlana Tyekucheva\n", "Maintainer": "Luigi Marchionni ", "Description": "the RTopper package is designed to perform and integrate\ngene set enrichment results across multiple genomic platforms.", "License": "GPL (>= 3) + file LICENSE", "biocViews": "Microarray", "LazyLoad": "yes", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:35:47 UTC", "RemoteUrl": "https://github.com/bioc/RTopper", "RemoteRef": "RELEASE_3_23", "RemoteSha": "984889152e39bb1467a4c628b7472293b635b075", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:53:26 UTC", "User": "root" }, "MD5sum": "952b3b05a79bfa6ef357ea73104ee122", "_user": "bioc-release", "_type": "src", "_file": "RTopper_1.58.0.tar.gz", "_fileid": "65a1de371cdfec96429968a79c8e632de6203eef84e644b37e8aecf65faf74a8", "_filesize": 1389708, "_sha256": "65a1de371cdfec96429968a79c8e632de6203eef84e644b37e8aecf65faf74a8", "_created": "2026-05-30T09:53:26.000Z", "_published": "2026-05-30T14:58:36.791Z", "_jobs": [ { "job": 78640935932, "time": 201, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307571844" }, { "job": 78640935969, "time": 193, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307571202" }, { "job": 78640935953, "time": 232, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307574623" }, { "job": 78640935945, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309050108" }, { "job": 78640935946, "time": 192, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309060611" }, { "job": 78640077590, "time": 235, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307327199" }, { "job": 78640935942, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307564863" }, { "job": 78640935984, "time": 404, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307592018" }, { "job": 78640935980, "time": 373, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307588472" }, { "job": 78640935973, "time": 342, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307585482" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RTopper", "_commit": { "id": "984889152e39bb1467a4c628b7472293b635b075", "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": 1777379747 }, "_maintainer": { "name": "Luigi Marchionni", "email": "marchion@jhu.edu", "login": "marchion", "description": "", "uuid": 1276265 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.12.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "limma", "role": "Imports" }, { "package": "multtest", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "KEGGREST", "role": "Suggests" }, { "package": "GO.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "microarray" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 500, "source": "https://www.bioconductor.org/packages/stats/bioc/RTopper" }, "_mentions": 1, "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RTopper.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "adjustPvalGSE", "combineGSE", "computeDrStat", "convertToDr", "runBatchGSE" ], "_datasets": [ { "name": "dat", "title": "A test dataset for the RTopper package", "object": "exampleData", "file": "exampleData.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "fgsList", "title": "A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package", "object": "fgsList", "file": "fgsList.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "gseResultsSep", "title": "A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package", "object": "gseResultsSep", "file": "gseResultsSep.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "intScores", "title": "A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package", "object": "intScores", "file": "intScores.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "pheno", "title": "A test dataset for the RTopper package", "object": "exampleData", "file": "exampleData.rda", "class": [ "data.frame" ], "fields": [ "Sample", "Class" ], "rows": 95, "table": true, "tojson": true }, { "name": "sepScores", "title": "A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package", "object": "sepScores", "file": "sepScores.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "RTopper-package", "title": "A package to perform run Gene Set Enrichment across genomic platforms", "topics": [ "RTopper-package", "RTopper" ] }, { "page": "adjustPvalGSE", "title": "Multiple testing correction", "topics": [ "adjustPvalGSE" ] }, { "page": "combineGSE", "title": "Combines GSE results", "topics": [ "combineGSE" ] }, { "page": "computeDrStat", "title": "Computes gene-to-phenotype associations scores", "topics": [ "computeDrStat" ] }, { "page": "convertToDr", "title": "Converts genomic data to a list suitable for computing gene-to-phenotype scores", "topics": [ "convertToDr" ] }, { "page": "dat", "title": "A test dataset for the RTopper package", "topics": [ "dat" ] }, { "page": "fgsList", "title": "A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package", "topics": [ "fgsList" ] }, { "page": "gseResultsSep", "title": "A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package", "topics": [ "gseResultsSep" ] }, { "page": "intScores", "title": "A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package", "topics": [ "intScores" ] }, { "page": "pheno", "title": "A test dataset for the RTopper package", "topics": [ "pheno" ] }, { "page": "runBatchGSE", "title": "To perform GSE analysis over multipple experiments and functional themes", "topics": [ "runBatchGSE" ] }, { "page": "sepScores", "title": "A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package", "topics": [ "sepScores" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics", "lattice", "limma", "MASS", "Matrix", "multtest", "statmod", "survival" ], "_vignettes": [ { "source": "RTopper.Rnw", "filename": "RTopper.pdf", "title": "RTopper user's manual", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:20:41", "modified": "2022-11-04 18:45:46", "commits": 6 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "rtopper", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/RTopper", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.58.0", "date": "2026-05-30T10:38:00.000Z", "distro": "noble", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "cdcb1b5f23a2ac9895e450ef99df4e61bb2fcf364e003f64a050f37412abadaf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.6.0", "os": "linux", "version": "1.58.0", "date": "2026-05-30T10:38:41.000Z", "distro": "noble", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "061a1ffd11524e16b3dfb4909cadfe2ee3eb302cb84931801deb4b0e6a0ddcd0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.5.3", "os": "mac", "version": "1.58.0", "date": "2026-05-30T14:56:15.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "963a6a6fc2c4323e811dcec78a4793cb462118ce6378405c1559debeff24f993", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.6.0", "os": "mac", "version": "1.58.0", "date": "2026-05-30T14:57:31.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "47d58acc5b58d618184aa589ccb2175720ef6ec2ddc829626c4ea9de1236eddc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.6.0", "os": "wasm", "version": "1.58.0", "date": "2026-05-30T10:37:40.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "4cc8936d4330a562eca55b3a317c7e381c58722ab53443d9ec0e580545386acb", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.7.0", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:41:21.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "e6f2e9c93f2a3b3b88a7a529764ee76a9d555121c1f83cdc0580eb63ba287fd4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.5.3", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:40:50.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "0cc3a4d4f2902d318c9d2991bf81ea1bdd89682bc0a99a47d8cab542c945f8f9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" }, { "r": "4.6.0", "os": "win", "version": "1.58.0", "date": "2026-05-30T10:40:39.000Z", "commit": "984889152e39bb1467a4c628b7472293b635b075", "fileid": "ec92528b41580c12788a85f6920d75f42baec5448f5ffa6550b90d8ac031fa1b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680235211" } ] }