{ "_id": "6a1d55f31d7bb097a0a46e3d", "Package": "GOstats", "Title": "Tools for manipulating GO and microarrays", "Version": "2.78.0", "Authors@R": "c(\nperson(\"Robert\", \"Gentleman\", role=\"aut\"),\nperson(\"Seth\", \"Falcon\", role=\"ctb\"),\nperson(\"Robert\", \"Castelo\", role=\"ctb\"),\nperson(\"Sonali\", \"Kumari\", role=\"ctb\",\ncomment=\"Converted vignettes from Sweave to R Markdown / HTML.\"),\nperson(\"Dennis\", \"Ndubi\", role=\"ctb\",\ncomment=\"Converted GOstatsHyperG vignette from Sweave to R Markdown / HTML.\"),\nperson(\"Bioconductor Package Maintainer\", role=\"cre\",\nemail=\"maintainer@bioconductor.org\"))", "Description": "A set of tools for interacting with GO and microarray\ndata. A variety of basic manipulation tools for graphs,\nhypothesis testing and other simple calculations.", "License": "Artistic-2.0", "Collate": "zzz.R AllClasses.R AllGenerics.R hyperGTest-methods.R\nGOHyperGResult-accessors.R GOgraph.R GOhyptest.R hyperGtable.R\nshortestPath.R triad.R OBOHyperGResult-accessors.R", "biocViews": "Annotation, GO, MultipleComparison, GeneExpression,\nMicroarray, Pathways, GeneSetEnrichment, GraphAndNetwork", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:30:38 UTC", "RemoteUrl": "https://github.com/bioc/GOstats", "RemoteRef": "RELEASE_3_23", "RemoteSha": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 09:41:15 UTC", "User": "root" }, "Author": "Robert Gentleman [aut],\nSeth Falcon [ctb],\nRobert Castelo [ctb],\nSonali Kumari [ctb] (Converted vignettes from Sweave to R Markdown /\nHTML.),\nDennis Ndubi [ctb] (Converted GOstatsHyperG vignette from Sweave to R\nMarkdown / HTML.),\nBioconductor Package Maintainer [cre]", "Maintainer": "Bioconductor Package Maintainer ", "MD5sum": "3f3cebe89911f3e88750762d65dc7bc9", "_user": "bioc-release", "_type": "src", "_file": "GOstats_2.78.0.tar.gz", "_fileid": "7c71da8c49a9112fd513d095bd80bac55137cdbcfc693927c5fbe29f39d52a4e", "_filesize": 1754099, "_sha256": "7c71da8c49a9112fd513d095bd80bac55137cdbcfc693927c5fbe29f39d52a4e", "_created": "2026-06-01T09:41:15.000Z", "_published": "2026-06-01T09:50:43.219Z", "_jobs": [ { "job": 78825859823, "time": 211, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7328260427" }, { "job": 78825859843, "time": 412, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7328329123" }, { "job": 78825859834, "time": 514, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7328365010" }, { "job": 78825859831, "time": 275, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7328281365" }, { "job": 78825859827, "time": 271, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7328280472" }, { "job": 78824254229, "time": 592, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7328190750" }, { "job": 78825859838, "time": 193, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7328254517" }, { "job": 78825860051, "time": 303, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7328291355" }, { "job": 78825859993, "time": 257, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7328275802" }, { "job": 78825859914, "time": 299, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7328289769" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GOstats", "_commit": { "id": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "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": 1777379438 }, "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Biobase", "version": ">= 1.15.29", "role": "Depends" }, { "package": "Category", "version": ">= 2.43.2", "role": "Depends" }, { "package": "graph", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stats4", "role": "Imports" }, { "package": "AnnotationDbi", "version": ">= 0.0.89", "role": "Imports" }, { "package": "GO.db", "version": ">= 1.13.0", "role": "Imports" }, { "package": "RBGL", "role": "Imports" }, { "package": "annotate", "version": ">= 1.13.2", "role": "Imports" }, { "package": "AnnotationForge", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "hgu95av2.db", "version": ">= 1.13.0", "role": "Suggests" }, { "package": "ALL", "role": "Suggests" }, { "package": "multtest", "role": "Suggests" }, { "package": "genefilter", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "xtable", "role": "Suggests" }, { "package": "SparseM", "role": "Suggests" }, { "package": "GSEABase", "role": "Suggests" }, { "package": "geneplotter", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 10, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.79.0", "bioc": "3.24" }, { "branch": "release", "version": "2.78.0", "bioc": "3.23" } ], "_topics": [ "annotation", "go", "multiplecomparison", "geneexpression", "microarray", "pathways", "genesetenrichment", "graphandnetwork" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 2394, "source": "https://www.bioconductor.org/packages/stats/bioc/GOstats" }, "_mentions": 368, "_searchresults": 624, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GOstats.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotation", "compCorrGraph", "compGdist", "description", "enumPairs", "expectedCounts", "geneCounts", "geneIds", "geneIdUniverse", "geneMappedCount", "goDag", "GOGraph", "htmlReport", "hyperGTest", "idx2dimnames", "inducedTermGraph", "isTriad", "makeGOGraph", "notConn", "oddsRatios", "oneGOGraph", "plotGOTermGraph", "probeSetSummary", "pvalues", "reduce2Degreek", "shortestPath", "simLL", "simLP", "simUI", "summary", "termGraphs", "testName", "triadCensus", "universeCounts", "universeMappedCount" ], "_datasets": [ { "name": "Bdists", "title": "Distance matrices for the BCR/ABL and NEG subgroups.", "object": "Bdists", "file": "Bdists.rda", "class": [ "matrix", "array" ], "fields": [ "39069_at", "40516_at", "36896_s_at", "287_at", "41235_at", "1863_s_at", "32253_at", "39147_g_at", "31895_at", "40091_at", "38740_at", "32588_s_at", "40202_at", "31519_f_at", "943_at", "41442_at", "106_at", "41175_at", "38354_at", "41000_at", "37535_at", "33831_at", "39438_at", "32067_at", "31823_at", "39420_at", "32168_s_at", "36630_at", "41632_at", "1703_g_at", "1044_s_at", "40375_at", "40067_at", "507_s_at", "31845_at", "38496_at", "33896_at", "914_g_at", "1519_at", "34818_at", "1638_at", "34715_at", "40570_at", "34740_at", "41425_at", "40268_at", "35943_s_at", "40511_at", "1102_s_at", "869_at", "37381_g_at", "35450_s_at", "141_s_at", "37910_at", "31820_at", "38771_at", "34368_at", "37497_at", "1039_s_at", "599_at", "38065_at", "39704_s_at", "280_g_at", "40343_at", "39610_at", "202_at", "40818_at", "40476_s_at", "669_s_at", "37625_at", "478_g_at", "36412_s_at", "32583_at", "32786_at", "41484_r_at", "37280_at", "38944_at", "36953_at", "39926_at", "1981_s_at", "41747_s_at", "37710_at", "35434_at", "39037_at", "33249_at", "35145_at", "38945_at", "1854_at", "37724_at", "32187_at", "39143_at", "40822_at", "37179_at", "853_at", "440_at", "37544_at", "1377_at", "544_at", "34667_at", "37561_at", "37928_at", "33415_at", "32340_s_at", "37623_at", "41600_at", "32696_at", "40446_at", "39117_at", "40061_at", "34828_at", "40896_at", "35940_at", "2044_s_at", "1784_s_at", "1785_at", "1856_at", "1295_at", "570_at", "32144_at", "41852_at", "35777_at", "36899_at", "32579_at", "33131_at", "1341_at", "AFFX-HUMISGF3A/M97935_3_at", "39708_at", "906_at", "506_s_at", "41222_at", "34753_at", "142_at", "192_at", "868_at", "38426_at", "1073_at", "1373_at", "32025_at", "33440_at", "33873_at", "36191_at", "40084_at", "37757_at", "38805_at", "38374_at", "1939_at", "603_at", "32706_at", "518_at", "39112_at", "34481_at", "39756_g_at", "891_at", "32809_at", "41713_at", "40569_at", "932_i_at", "36295_at", "35368_at", "32034_at", "316_g_at", "36634_at", "40659_at", "33387_at", "39839_at", "1452_at", "40790_at", "34216_at", "39032_at", "39029_at", "32261_at", "1643_g_at", "40412_at", "36214_at", "41360_at", "37980_at", "670_s_at", "38146_at", "41788_i_at", "35681_r_at", "35352_at", "35705_at", "33425_at", "36825_at", "41526_at", "33113_at", "38517_at", "38518_at", "35824_at", "38142_at", "39077_at", "35319_at", "31364_i_at", "35614_at", "40691_at", "32654_g_at", "37837_at", "41503_at", "35163_at", "37336_at", "34394_at", "32241_at", "41649_at", "38311_at", "38641_at", "39698_at" ], "rows": 206, "table": true, "tojson": true }, { "name": "Ndists", "title": "Distance matrices for the BCR/ABL and NEG subgroups.", "object": "Ndists", "file": "Ndists.rda", "class": [ "matrix", "array" ], "fields": [ "39069_at", "40516_at", "36896_s_at", "287_at", "41235_at", "1863_s_at", "32253_at", "39147_g_at", "31895_at", "40091_at", "38740_at", "32588_s_at", "40202_at", "31519_f_at", "943_at", "41442_at", "106_at", "41175_at", "38354_at", "41000_at", "37535_at", "33831_at", "39438_at", "32067_at", "31823_at", "39420_at", "32168_s_at", "36630_at", "41632_at", "1703_g_at", "1044_s_at", "40375_at", "40067_at", "507_s_at", "31845_at", "38496_at", "33896_at", "914_g_at", "1519_at", "34818_at", "1638_at", "34715_at", "40570_at", "34740_at", "41425_at", "40268_at", "35943_s_at", "40511_at", "1102_s_at", "869_at", "37381_g_at", "35450_s_at", "141_s_at", "37910_at", "31820_at", "38771_at", "34368_at", "37497_at", "1039_s_at", "599_at", "38065_at", "39704_s_at", "280_g_at", "40343_at", "39610_at", "202_at", "40818_at", "40476_s_at", "669_s_at", "37625_at", "478_g_at", "36412_s_at", "32583_at", "32786_at", "41484_r_at", "37280_at", "38944_at", "36953_at", "39926_at", "1981_s_at", "41747_s_at", "37710_at", "35434_at", "39037_at", "33249_at", "35145_at", "38945_at", "1854_at", "37724_at", "32187_at", "39143_at", "40822_at", "37179_at", "853_at", "440_at", "37544_at", "1377_at", "544_at", "34667_at", "37561_at", "37928_at", "33415_at", "32340_s_at", "37623_at", "41600_at", "32696_at", "40446_at", "39117_at", "40061_at", "34828_at", "40896_at", "35940_at", "2044_s_at", "1784_s_at", "1785_at", "1856_at", "1295_at", "570_at", "32144_at", "41852_at", "35777_at", "36899_at", "32579_at", "33131_at", "1341_at", "AFFX-HUMISGF3A/M97935_3_at", "39708_at", "906_at", "506_s_at", "41222_at", "34753_at", "142_at", "192_at", "868_at", "38426_at", "1073_at", "1373_at", "32025_at", "33440_at", "33873_at", "36191_at", "40084_at", "37757_at", "38805_at", "38374_at", "1939_at", "603_at", "32706_at", "518_at", "39112_at", "34481_at", "39756_g_at", "891_at", "32809_at", "41713_at", "40569_at", "932_i_at", "36295_at", "35368_at", "32034_at", "316_g_at", "36634_at", "40659_at", "33387_at", "39839_at", "1452_at", "40790_at", "34216_at", "39032_at", "39029_at", "32261_at", "1643_g_at", "40412_at", "36214_at", "41360_at", "37980_at", "670_s_at", "38146_at", "41788_i_at", "35681_r_at", "35352_at", "35705_at", "33425_at", "36825_at", "41526_at", "33113_at", "38517_at", "38518_at", "35824_at", "38142_at", "39077_at", "35319_at", "31364_i_at", "35614_at", "40691_at", "32654_g_at", "37837_at", "41503_at", "35163_at", "37336_at", "34394_at", "32241_at", "41649_at", "38311_at", "38641_at", "39698_at" ], "rows": 206, "table": true, "tojson": true } ], "_help": [ { "page": "GOstats-package", "title": "Tools for manipulating GO and microarrays.", "topics": [ "GOstats-package", "GOstats" ] }, { "page": "compCorrGraph", "title": "A function to compute a correlation based graph from Gene Expression Data", "topics": [ "compCorrGraph" ] }, { "page": "compGdist", "title": "A function to compute the distance between pairs of nodes in a graph.", "topics": [ "compGdist" ] }, { "page": "GOHyperGResult-class", "title": "Class \"GOHyperGResult\"", "topics": [ "conditional,GOHyperGResult-method", "expectedCounts,GOHyperGResult-method", "geneCounts,GOHyperGResult-method", "geneIdUniverse,GOHyperGResult-method", "goDag", "goDag,GOHyperGResult-method", "GOHyperGResult-class", "htmlReport,GOHyperGResult-method", "oddsRatios,GOHyperGResult-method", "pvalues,GOHyperGResult-method", "summary,GOHyperGResult-method" ] }, { "page": "GOstats-defunct", "title": "Defunct Functions in GOstats Package", "topics": [ "combGOGraph", "getGoGraph", "GOHyperG", "GOKEGGHyperG", "GOLeaves", "GOstats-defunct", "hyperG2Affy", "hyperGtable", "selectedGenes" ] }, { "page": "hyperGTest", "title": "Hypergeometric Tests for GO term association", "topics": [ "hyperGTest", "hyperGTest,GOHyperGParams-method", "hyperGTest,OBOHyperGParams-method" ] }, { "page": "idx2dimnames", "title": "Index to Dimnames", "topics": [ "idx2dimnames" ] }, { "page": "makeGOGraph", "title": "Construct a GO Graph", "topics": [ "makeGOGraph" ] }, { "page": "Ndists", "title": "Distance matrices for the BCR/ABL and NEG subgroups.", "topics": [ "Bdists", "Ndists" ] }, { "page": "notConn", "title": "Find genes that are not connected to the others.", "topics": [ "notConn" ] }, { "page": "OBOHyperGResult-class", "title": "Class \"OBOHyperGResult\"", "topics": [ "conditional,OBOHyperGResult-method", "expectedCounts,OBOHyperGResult-method", "geneCounts,OBOHyperGResult-method", "geneIdUniverse,OBOHyperGResult-method", "goDag,OBOHyperGResult-method", "htmlReport,OBOHyperGResult-method", "OBOHyperGResult-class", "oddsRatios,OBOHyperGResult-method", "pvalues,OBOHyperGResult-method", "summary,OBOHyperGResult-method" ] }, { "page": "oneGOGraph", "title": "Construct the GO graph given a set of leaves.", "topics": [ "GOGraph", "oneGOGraph" ] }, { "page": "probeSetSummary", "title": "Summarize Probe Sets Associated with a hyperGTest Result", "topics": [ "probeSetSummary" ] }, { "page": "shortestPath", "title": "Shortest Path Analysis", "topics": [ "shortestPath" ] }, { "page": "simLL", "title": "Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs.", "topics": [ "simLL", "simLP", "simUI" ] }, { "page": "termGraphs", "title": "Extraction and Plotting of GO Terms from a GOHyperGResult Object", "topics": [ "inducedTermGraph", "plotGOTermGraph", "termGraphs" ] }, { "page": "triadCensus", "title": "Triad Functions", "topics": [ "enumPairs", "isTriad", "reduce2Degreek", "triad", "triadCensus" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "AnnotationForge", "askpass", "BH", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "Category", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "genefilter", "generics", "glue", "GO.db", "graph", "GSEABase", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "RBGL", "RCurl", "Rgraphviz", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_score": 6.952459986136461, "_indexed": false, "_nocasepkg": "gostats", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/GOstats", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.78.0", "date": "2026-06-01T09:46:07.000Z", "distro": "noble", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "1e551960fea827c530d08a47ec1f012f7360213e3a721fbc48d45237084304df", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.6.0", "os": "linux", "version": "2.78.0", "date": "2026-06-01T09:47:37.000Z", "distro": "noble", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "f59788d5ae0f884a2aab01043664172153e116056589ddc38371f7ad81721cd9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.5.3", "os": "mac", "version": "2.78.0", "date": "2026-06-01T09:44:06.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "9cacf347178dd5ad88e2e7ee56e5f400ccb390fbc7aaaa2804a9f8e2818e89b6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.6.0", "os": "mac", "version": "2.78.0", "date": "2026-06-01T09:44:03.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "1eb1b8d711a7c63f501405eca47c29b99b6c354ddc21541f307f49d96d7fe3c8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.6.0", "os": "wasm", "version": "2.78.0", "date": "2026-06-01T09:44:57.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "a50734b1559241935e0db65e780b40071cb32a2c1394e3977c2f54e2d6e475f0", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.7.0", "os": "win", "version": "2.78.0", "date": "2026-06-01T09:43:56.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "7fd4d175956fdcb91793e3512552c2d19e52755279bef9147ff6351ac717a788", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.5.3", "os": "win", "version": "2.78.0", "date": "2026-06-01T09:43:37.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "35b22244ea61a2fe90045535c0ef16ce995364447159c5ddfee6ac2e650688f7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" }, { "r": "4.6.0", "os": "win", "version": "2.78.0", "date": "2026-06-01T09:43:46.000Z", "commit": "c5035d6cd10f5cf0e4f999f3dcefe5593f8db665", "fileid": "7f81d297e491334f23a518777147337e38d406466294b9522c6f77934c276945", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26746787625" } ] }