{ "_id": "6a1049f9acfb0bcc41c9f972", "Package": "GoMiner", "Version": "1.3", "Date": "2025-06-04", "Title": "Automate the Mapping Between a List of Genes and Gene Ontology\nCategories", "Authors@R": "c(\nperson(\"Barry\", \"Zeeberg\", email = \"barryz2013@gmail.com\",\nrole = c(\"aut\", \"cre\")))", "Maintainer": "Barry Zeeberg ", "Author": "Barry Zeeberg [aut, cre]", "LazyData": "true", "LazyDataCompression": "xz", "Description": "In gene-expression microarray studies, for example, one\ngenerally obtains a list of dozens or hundreds of genes that\ndiffer in expression between samples and then asks 'What does\nall of this mean biologically?' Alternatively, gene lists can\nbe derived conceptually in addition to experimentally. For\ninstance, one might want to analyze a group of genes known as\nhousekeeping genes. The work of the Gene Ontology (GO)\nConsortium provides a way to address that\nquestion. GO organizes genes into hierarchical categories based\non biological process, molecular function and subcellular\nlocalization. The role of 'GoMiner' is to automate the mapping\nbetween a list of genes and GO, and to provide a statistical\nsummary of the results as well as a visualization.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 08:29:13 UTC", "User": "root" }, "Repository": "https://barryzee.r-universe.dev", "Date/Publication": "2025-06-05 23:10:02 UTC", "RemoteUrl": "https://github.com/cran/GoMiner", "RemoteRef": "HEAD", "RemoteSha": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "MD5sum": "be3bc7ce61b1cb636fb65516747e32bc", "_user": "barryzee", "_type": "src", "_file": "GoMiner_1.3.tar.gz", "_fileid": "89803fe8fbc2c233bf2408fc724d79e039e1cfb6d25468da422767b8d3789267", "_filesize": 3664310, "_sha256": "89803fe8fbc2c233bf2408fc724d79e039e1cfb6d25468da422767b8d3789267", "_created": "2026-05-10T08:29:13.000Z", "_published": "2026-05-22T12:20:09.148Z", "_distro": "noble", "_jobs": [ { "job": 77378047221, "time": 145, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6902324211" }, { "job": 77378047055, "time": 130, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902322808" }, { "job": 77378046972, "time": 96, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6902393558" }, { "job": 77378046984, "time": 90, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902391650" }, { "job": 77378046637, "time": 207, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902310537" }, { "job": 77378046424, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160312755" }, { "job": 77378047029, "time": 114, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6902321281" }, { "job": 77378047071, "time": 83, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6902318400" }, { "job": 77378047139, "time": 96, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6902319613" } ], "_buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/GoMiner", "_commit": { "id": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "author": "Barry Zeeberg ", "committer": "cran-robot ", "message": "version 1.3\n", "time": 1749165002 }, "_maintainer": { "name": "Barry Zeeberg", "email": "barryz2013@gmail.com", "login": "barryzee", "uuid": 75148535 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "minimalistGODB", "role": "Imports" }, { "package": "HGNChelper", "role": "Imports" }, { "package": "randomGODB", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vprint", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-20", "n": 2 }, { "week": "2025-23", "n": 1 } ], "_tags": [ { "name": "1.1", "date": "2025-05-13" }, { "name": "1.2", "date": "2025-05-18" }, { "name": "1.3", "date": "2025-06-05" } ], "_stars": 0, "_contributors": [ { "user": "barryzee", "count": 4, "uuid": 75148535 } ], "_userbio": { "uuid": 75148535, "type": "user", "name": "barryzee" }, "_downloads": { "count": 582, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GoMiner" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GoMiner.html", "manual.pdf" ], "_realowner": "barryzee", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2025-03-25" }, { "version": "1.1", "date": "2025-05-13" }, { "version": "1.2", "date": "2025-05-18" }, { "version": "1.3", "date": "2025-06-06" } ], "_exports": [ "checkGeneListVsDB", "FDR", "GOenrich3", "GOheatmap", "GOhypergeometric3", "GoMiner", "GOtable3", "GOthresh", "hitterBeforeAfterDriver", "hitters2", "human", "preprocessDB", "randSubsetGeneList", "RCPD", "runGoMinerExamples", "trimGOGOA3", "validHGNCSymbols" ], "_datasets": [ { "name": "cluster52", "title": "GoMiner data set", "object": "cluster52", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "GOGOA3small", "title": "GoMiner data set", "object": "GOGOA3small", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "HCCS66", "title": "GoMiner data set", "object": "HCCS66", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Housekeeping_Genes", "title": "GoMiner data set", "object": "Housekeeping_Genes", "class": [ "data.frame" ], "fields": [ "Ensembl", "Gene.name", "Refseq", "CCDS.ID" ], "rows": 2833, "table": true, "tojson": true }, { "name": "x_fdr", "title": "GoMiner data set", "object": "x_fdr", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "x_hyper1", "title": "GoMiner data set", "object": "x_hyper1", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "x_m", "title": "GoMiner data set", "object": "x_m", "class": [ "matrix", "array" ], "fields": [ "SAMPLE", "POP", "ENRICHMENT" ], "rows": 802, "table": true, "tojson": true }, { "name": "x_sampleList1", "title": "GoMiner data set", "object": "x_sampleList1", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "x_tablePop3", "title": "GoMiner data set", "object": "x_tablePop3", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "x_tablePop31", "title": "GoMiner data set", "object": "x_tablePop31", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "x_tableSample3", "title": "GoMiner data set", "object": "x_tableSample3", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "x_thresh", "title": "GoMiner data set", "object": "x_thresh", "class": [ "data.frame" ], "fields": [ "Row.names", "SAMPLE", "POP", "ENRICHMENT", "OBSERVED_LOG10(P)", "FDR" ], "rows": 18, "table": true, "tojson": true } ], "_help": [ { "page": "checkGeneListVsDB", "title": "checkGeneListVsDB", "topics": [ "checkGeneListVsDB" ] }, { "page": "cluster52", "title": "GoMiner data set", "topics": [ "cluster52" ] }, { "page": "FDR", "title": "FDR", "topics": [ "FDR" ] }, { "page": "GOenrich3", "title": "GOenrich3", "topics": [ "GOenrich3" ] }, { "page": "GOGOA3small", "title": "GoMiner data set", "topics": [ "GOGOA3small" ] }, { "page": "GOheatmap", "title": "GOheatmap", "topics": [ "GOheatmap" ] }, { "page": "GOhypergeometric3", "title": "GOhypergeometric", "topics": [ "GOhypergeometric3" ] }, { "page": "GoMiner", "title": "GoMiner", "topics": [ "GoMiner" ] }, { "page": "GOtable3", "title": "GOtable3", "topics": [ "GOtable3" ] }, { "page": "GOthresh", "title": "GOthresh", "topics": [ "GOthresh" ] }, { "page": "HCCS66", "title": "GoMiner data set", "topics": [ "HCCS66" ] }, { "page": "hitterBeforeAfterDriver", "title": "hitterBeforeAfterDriver", "topics": [ "hitterBeforeAfterDriver" ] }, { "page": "hitters2", "title": "hitters2", "topics": [ "hitters2" ] }, { "page": "Housekeeping_Genes", "title": "GoMiner data set", "topics": [ "Housekeeping_Genes" ] }, { "page": "human", "title": "human", "topics": [ "human" ] }, { "page": "preprocessDB", "title": "preprocessDB", "topics": [ "preprocessDB" ] }, { "page": "randSubsetGeneList", "title": "randSubsetGeneList", "topics": [ "randSubsetGeneList" ] }, { "page": "RCPD", "title": "RCPD", "topics": [ "RCPD" ] }, { "page": "runGoMinerExamples", "title": "runGoMinerExamples", "topics": [ "runGoMinerExamples" ] }, { "page": "trimGOGOA3", "title": "trimGOGOA3", "topics": [ "trimGOGOA3" ] }, { "page": "validHGNCSymbols", "title": "validHGNCSymbols", "topics": [ "validHGNCSymbols" ] }, { "page": "x_fdr", "title": "GoMiner data set", "topics": [ "x_fdr" ] }, { "page": "x_hyper1", "title": "GoMiner data set", "topics": [ "x_hyper1" ] }, { "page": "x_m", "title": "GoMiner data set", "topics": [ "x_m" ] }, { "page": "x_sampleList1", "title": "GoMiner data set", "topics": [ "x_sampleList1" ] }, { "page": "x_tablePop3", "title": "GoMiner data set", "topics": [ "x_tablePop3" ] }, { "page": "x_tablePop31", "title": "GoMiner data set", "topics": [ "x_tablePop31" ] }, { "page": "x_tableSample3", "title": "GoMiner data set", "topics": [ "x_tableSample3" ] }, { "page": "x_thresh", "title": "GoMiner data set", "topics": [ "x_thresh" ] } ], "_rundeps": [ "bitops", "caTools", "data.table", "gplots", "gtools", "HGNChelper", "KernSmooth", "minimalistGODB", "randomGODB", "splitstackshape", "vprint" ], "_vignettes": [ { "source": "GoMiner.Rmd", "filename": "GoMiner.html", "title": "GoMiner", "author": "Barry Zeeberg [aut, cre]", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-03-25 09:20:02", "modified": "2025-05-13 23:20:02", "commits": 2 } ], "_score": 3.3802112417116064, "_indexed": true, "_nocasepkg": "gominer", "_universes": [ "barryzee" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3", "date": "2026-05-10T08:31:37.000Z", "distro": "noble", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "82fe7ff0275bab0e586dea309a09a021c0dfe0bad0391aafa3e4c902827a95f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.6.0", "os": "linux", "version": "1.3", "date": "2026-05-10T08:31:29.000Z", "distro": "noble", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "5f5cb0d8a7b57e2f4bb731ba20b2d5049eefda4856bf8daa8ea0eba9b0c51bb9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.5.3", "os": "mac", "version": "1.3", "date": "2026-05-10T08:43:15.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "a99c3f1aec1c3ea2d8de15e74895bdac5f56afc1a4ed5c071cc7fc20b608fdaa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.6.0", "os": "mac", "version": "1.3", "date": "2026-05-10T08:42:59.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "563ac22c12f6693f9c4357001aceea3f1cc8bd952c1c0daae3e7f805bf622600", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.7.0", "os": "win", "version": "1.3", "date": "2026-05-10T08:31:07.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "fd2d35e3df25f0bce2e82f97de089656c9fddf22edb4fa5e40fa09000cef18d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.5.3", "os": "win", "version": "1.3", "date": "2026-05-10T08:30:34.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "fa3e33b6330f627d3eb5fcc55e9ec39c87f222bf7cb56fe2b5233f78caf3dc06", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.6.0", "os": "win", "version": "1.3", "date": "2026-05-10T08:30:49.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "9aa35690e483c51c248edb883a39424e7bd1a0167e825ad1f16c927793c6bee7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" }, { "r": "4.6.0", "os": "wasm", "version": "1.3", "date": "2026-05-22T12:19:41.000Z", "commit": "0a6433fd9c6f3548d0c451a1c64a73dbb8b91c71", "fileid": "6bc1948e5dd62e16e6494b371fd021b18413446e84da983c83a89930ac666b00", "status": "success", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/25624003527" } ] }