{ "_id": "6a105e7cacfb0bcc41ca5a1a", "Package": "globaltest", "Version": "5.67.0", "Date": "2023-03-30", "Title": "Testing Groups of Covariates/Features for Association with a\nResponse Variable, with Applications to Gene Set Testing", "Author": "Jelle Goeman and Jan Oosting, with contributions by Livio\nFinos, Aldo Solari, Dominic Edelmann", "Maintainer": "Jelle Goeman ", "Description": "The global test tests groups of covariates (or features)\nfor association with a response variable. This package\nimplements the test with diagnostic plots and multiple testing\nutilities, along with several functions to facilitate the use\nof this test for gene set testing of GO and KEGG terms.", "License": "GPL (>= 2)", "biocViews": "Microarray, OneChannel, Bioinformatics,\nDifferentialExpression, GO, Pathways", "Collate": "gt-object.R mlogit.R comparative.R diagnosticplots.R\nfocuslevel.R generalizedFdistribution.R genesettesting.R gt.R\ninheritance.R models.R options.R utilities.R goodnessoffit.R", "LazyLoad": "yes", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:30:41 UTC", "RemoteUrl": "https://github.com/bioc/globaltest", "RemoteRef": "HEAD", "RemoteSha": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-08 09:22:11 UTC", "User": "root" }, "MD5sum": "72c9ee43095fca7b67a380ff1d6af2de", "_user": "bioc", "_type": "src", "_file": "globaltest_5.67.0.tar.gz", "_fileid": "70d6c9909bca9e918c0a1534e275af6a20852ad2c481c31a26ac7b25a10a1c7b", "_filesize": 748001, "_sha256": "70d6c9909bca9e918c0a1534e275af6a20852ad2c481c31a26ac7b25a10a1c7b", "_created": "2026-05-08T09:22:11.000Z", "_published": "2026-05-22T13:47:40.409Z", "_jobs": [ { "job": 77392447302, "time": 223, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "6876006547" }, { "job": 77392447082, "time": 311, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6876034251" }, { "job": 77392447367, "time": 325, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6876037539" }, { "job": 77392447343, "time": 233, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6876202912" }, { "job": 77392447464, "time": 148, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6876156417" }, { "job": 77392447571, "time": 402, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6875941609" }, { "job": 77392446404, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7162061535" }, { "job": 77392447007, "time": 229, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6876009141" }, { "job": 77392447626, "time": 202, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6876001544" }, { "job": 77392447128, "time": 202, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6876000438" } ], "_bioccheck": { "error": 2, "warning": 7, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/globaltest", "_commit": { "id": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379441 }, "_maintainer": { "name": "Jelle Goeman", "email": "j.j.goeman@lumc.nl", "login": "jellegoeman", "uuid": 24312915 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "survival", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "annotate", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "vsn", "role": "Suggests" }, { "package": "golubEsets", "role": "Suggests" }, { "package": "KEGGREST", "role": "Suggests" }, { "package": "hu6800.db", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" }, { "package": "GO.db", "role": "Suggests" }, { "package": "lungExpression", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "GSEABase", "role": "Suggests" }, { "package": "penalized", "role": "Suggests" }, { "package": "gss", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "boot", "role": "Suggests" }, { "package": "rpart", "role": "Suggests" }, { "package": "mstate", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 7, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "5.67.0", "bioc": "3.24" }, { "branch": "release", "version": "5.66.0", "bioc": "3.23" } ], "_topics": [ "microarray", "onechannel", "bioinformatics", "differentialexpression", "go", "pathways" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 2278, "source": "https://www.bioconductor.org/packages/stats/bioc/globaltest" }, "_mentions": 30, "_searchresults": 84, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/globaltest.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "alias", "alias<-", "bbase", "btensor", "coefficients", "combine", "comparative", "covariates", "draw", "extract", "features", "findFocus", "fitted.values", "focusLevel", "gt", "gt.options", "gtBroad", "gtConcept", "gtGO", "gtKEGG", "gtKS", "gtLI", "gtPS", "hist", "inheritance", "leafNodes", "mlogit", "model.matrix", "p.adjust", "p.value", "reparamZ", "residuals", "result", "reweighZ", "show", "size", "sort", "sterms", "subjects", "subsets", "summary", "weights", "z.score" ], "_help": [ { "page": "comparative", "title": "Comparative proportions for the Global Test", "topics": [ "comparative" ] }, { "page": "diagnostics", "title": "Global Test diagnostic plots", "topics": [ "covariates", "diagnostics", "features", "subjects" ] }, { "page": "gt", "title": "Global Test", "topics": [ "globaltest", "gt" ] }, { "page": "genesettesting", "title": "Gene set testing of gene set databases using Global Test", "topics": [ "gtBroad", "gtConcept", "gtGO", "gtKEGG", "gtKEGGREST" ] }, { "page": "goodnessoffit", "title": "Goodness of fit testing in regression models using Global Test", "topics": [ "bbase", "btensor", "gtKS", "gtLI", "gtPS", "reparamZ", "reweighZ", "sterms" ] }, { "page": "gt.object-class", "title": "Class \"gt.object\" for storing the result of the function gt", "topics": [ "alias,gt.object-method", "alias<-", "alias<-,gt.object-method", "extract", "extract,gt.object-method", "gt.object", "gt.object-class", "hist,gt.object-method", "length,gt.object-method", "model.matrix,gt.object-method", "names,gt.object-method", "names<-,gt.object-method", "p.adjust,gt.object-method", "p.value", "p.value,gt.object-method", "result", "result,gt.object-method", "show,gt.object-method", "size", "size,gt.object-method", "sort,gt.object-method", "sterms,gt.object-method", "subsets", "subsets,gt.object-method", "summary,gt.object-method", "weights,gt.object-method", "z.score", "z.score,gt.object-method", "[,gt.object,ANY,ANY,ANY-method", "[,gt.object-method", "[[,gt.object-method" ] }, { "page": "gtoptions", "title": "Options for globaltest package", "topics": [ "gt.options" ] }, { "page": "mlogit", "title": "Multinomial Logistic Regression", "topics": [ "coefficients,mlogit-method", "fitted.values,mlogit-method", "mlogit", "mlogit-class", "residuals,mlogit-method", "show,mlogit-method", "summary,mlogit-method" ] }, { "page": "multtest", "title": "Multiple testing correction for the Global Test", "topics": [ "draw", "findFocus", "focusLevel", "inheritance", "leafNodes" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "Matrix", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "GlobalTest.Rnw", "filename": "GlobalTest.pdf", "title": "Global Test", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:52:09", "modified": "2020-04-07 13:12:46", "commits": 3 } ], "_score": 6.905082296202864, "_indexed": true, "_nocasepkg": "globaltest", "_universes": [ "bioc", "jellegoeman" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "5.67.0", "date": "2026-05-08T09:26:24.000Z", "distro": "noble", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "ca578ca0c07ae6d9aa676b0c6bbfae652389c9ba5752a9774dd0f279a6c640fc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.6.0", "os": "linux", "version": "5.67.0", "date": "2026-05-08T09:26:33.000Z", "distro": "noble", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "5db060cd7bf21fc64205d80bddd09b72c0480d9e3e57673fbf33789836c65e01", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.5.3", "os": "mac", "version": "5.67.0", "date": "2026-05-08T09:36:20.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "f82c8ddf52055f40239109d5996707da46804c0b59328a19c578cb54d224ae90", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.6.0", "os": "mac", "version": "5.67.0", "date": "2026-05-08T09:34:13.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "e33ae3906d0f86dba4e727266fe43b312c79bb0550292ea6c77ff0de19cc0e98", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.7.0", "os": "win", "version": "5.67.0", "date": "2026-05-08T09:24:44.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "d15f67f7bcf54b4a36463a142ad4d1e1866b201c2ff38d453c55c0fa5c2b2bf2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.5.3", "os": "win", "version": "5.67.0", "date": "2026-05-08T09:24:27.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "76d736a532a1b3014d86291b86085220f393ddc8cb9f9f897e9e14ff626ab50e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.6.0", "os": "win", "version": "5.67.0", "date": "2026-05-08T09:24:22.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "e8e783eea14d7c98d53f9183dbb569a22904e34763659e317cdfba389ea0d59c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" }, { "r": "4.6.0", "os": "wasm", "version": "5.67.0", "date": "2026-05-22T13:47:17.000Z", "commit": "54324cc1d14e6cbd5edb3d6a8c651f1c6870de3d", "fileid": "b2918ce71d3368850ce5d1048fe31ed26c3dc1a748c7e107d6081e9156388b23", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25547507129" } ] }