{ "_id": "6a1982e4acfb0bcc41df9e61", "Package": "DOSE", "Type": "Package", "Title": "Disease Ontology Semantic and Enrichment analysis", "Version": "4.7.0", "Authors@R": "c( person(given = \"Guangchuang\", family = \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Li-Gen\", family = \"Wang\", email = \"reeganwang020@gmail.com\", role = \"ctb\"),\nperson(given = \"Vladislav\", family = \"Petyuk\", email = \"petyuk@gmail.com\", role = \"ctb\"),\nperson(given = \"Giovanni\", family = \"Dall'Olio\", email = \"giovanni.dallolio@upf.edu\", role = \"ctb\"))", "Maintainer": "Guangchuang Yu ", "Description": "This package implements five methods proposed by Resnik,\nSchlicker, Jiang, Lin and Wang respectively for measuring\nsemantic similarities among DO terms and gene products.\nEnrichment analyses including hypergeometric model and gene set\nenrichment analysis are also implemented for discovering\ndisease associations of high-throughput biological data.", "VignetteBuilder": "knitr", "ByteCompile": "true", "License": "Artistic-2.0", "Encoding": "UTF-8", "URL": "https://yulab-smu.top/contribution-knowledge-mining/", "BugReports": "https://github.com/GuangchuangYu/DOSE/issues", "Packaged": { "Date": "2026-05-29 10:30:59 UTC", "User": "root" }, "biocViews": "Annotation, Visualization, MultipleComparison,\nGeneSetEnrichment, Pathways, Software", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:30 UTC", "RemoteUrl": "https://github.com/bioc/DOSE", "RemoteRef": "HEAD", "RemoteSha": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "NeedsCompilation": "no", "Author": "Guangchuang Yu [aut, cre],\nLi-Gen Wang [ctb],\nVladislav Petyuk [ctb],\nGiovanni Dall'Olio [ctb]", "MD5sum": "2192d83bed788a314b25e77be578410c", "_user": "bioc", "_type": "src", "_file": "DOSE_4.7.0.tar.gz", "_fileid": "346221fdbe146ef6dcf707e52d7897cfe2bdee159c91b6462621ebdb3fc8ec87", "_filesize": 5810018, "_sha256": "346221fdbe146ef6dcf707e52d7897cfe2bdee159c91b6462621ebdb3fc8ec87", "_created": "2026-05-29T10:30:59.000Z", "_published": "2026-05-29T12:13:24.440Z", "_jobs": [ { "job": 78483830568, "time": 203, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7288688535" }, { "job": 78483830556, "time": 294, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7288714340" }, { "job": 78483830571, "time": 282, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7288711112" }, { "job": 78483830578, "time": 134, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7290354242" }, { "job": 78483830558, "time": 161, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7290362716" }, { "job": 78483182706, "time": 272, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288629642" }, { "job": 78483830572, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288674974" }, { "job": 78483830580, "time": 201, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7288688637" }, { "job": 78483830555, "time": 188, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7288684410" }, { "job": 78483830593, "time": 329, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7288724498" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DOSE", "_commit": { "id": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379730 }, "_maintainer": { "name": "Guangchuang Yu", "email": "guangchuangyu@gmail.com", "login": "guangchuangyu", "twitter": "@guangchuangyu", "description": "Professor of Bioinformatics at Southern Medical University.", "uuid": 626539 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "enrichit", "version": ">= 0.0.4", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "GOSemSim", "version": ">= 2.37.1", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "yulab.utils", "version": "> 0.2.2", "role": "Imports" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "gson", "version": ">= 0.0.5", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "memoise", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 61, "_updates": [ { "week": "2025-39", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-49", "n": 4 }, { "week": "2025-50", "n": 17 }, { "week": "2025-52", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "4.7.0", "bioc": "3.24" }, { "branch": "release", "version": "4.6.0", "bioc": "3.23" } ], "_topics": [ "annotation", "visualization", "multiplecomparison", "genesetenrichment", "pathways", "software", "disease-ontology", "enrichment-analysis", "semantic-similarity" ], "_stars": 126, "_contributors": [ { "user": "guangchuangyu", "count": 866, "uuid": 626539 }, { "user": "huerqiang", "count": 78, "uuid": 48857018 }, { "user": "dtenenba", "count": 33, "uuid": 2286826 }, { "user": "nturaga", "count": 18, "uuid": 2746443 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "dalloliogm", "count": 14, "uuid": 14500 }, { "user": "vladpetyuk", "count": 8, "uuid": 4207635 }, { "user": "llrs", "count": 6, "uuid": 6818218 }, { "user": "gregkoytiger", "count": 6, "uuid": 15109034 }, { "user": "hpages", "count": 4, "uuid": 8810451 }, { "user": "vobencha", "count": 4, "uuid": 2466173 }, { "user": "lgatto", "count": 3, "uuid": 384198 }, { "user": "clearmind777", "count": 2, "uuid": 139222736 }, { "user": "pedrostrusso", "count": 2, "uuid": 10830114 }, { "user": "alexyfyf", "count": 1, "uuid": 24263494 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 43056, "source": "https://www.bioconductor.org/packages/stats/bioc/DOSE" }, "_mentions": 138, "_devurl": "https://github.com/guangchuangyu/dose", "_searchresults": 3344, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DOSE.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yulab-smu/dose", "_realowner": "bioc", "_cranurl": false, "_exports": [ "clusterSim", "doseSim", "doSim", "enrichDGN", "enrichDGNv", "enrichDO", "enrichNCG", "facet_grid", "gene2DO", "geneSim", "get_organism", "gseDGN", "gseDO", "gseNCG", "mclusterSim", "simplot", "theme_dose" ], "_datasets": [ { "name": "DGN_EXTID2PATHID", "title": "Datasets", "object": "DGN_EXTID2PATHID", "file": "DGN_EXTID2PATHID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "DGN_PATHID2EXTID", "title": "Datasets", "object": "DGN_PATHID2EXTID", "file": "DGN_PATHID2EXTID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "DGN_PATHID2NAME", "title": "Datasets", "object": "DGN_PATHID2NAME", "file": "DGN_PATHID2NAME.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "geneList", "title": "Datasets", "object": "geneList", "file": "geneList.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "NCG_EXTID2PATHID", "title": "Datasets", "object": "NCG_EXTID2PATHID", "file": "NCG_EXTID2PATHID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "NCG_PATHID2EXTID", "title": "Datasets", "object": "NCG_PATHID2EXTID", "file": "NCG_PATHID2EXTID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "VDGN_EXTID2PATHID", "title": "Datasets", "object": "VDGN_EXTID2PATHID", "file": "VDGN_EXTID2PATHID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "VDGN_PATHID2EXTID", "title": "Datasets", "object": "VDGN_PATHID2EXTID", "file": "VDGN_PATHID2EXTID.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "VDGN_PATHID2NAME", "title": "Datasets", "object": "VDGN_PATHID2NAME", "file": "VDGN_PATHID2NAME.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "clusterSim", "title": "clusterSim", "topics": [ "clusterSim" ] }, { "page": "computeIC", "title": "compute information content", "topics": [ "computeIC" ] }, { "page": "DataSet", "title": "Datasets", "topics": [ "DataSet", "DGN_EXTID2PATHID", "DGN_PATHID2EXTID", "DGN_PATHID2NAME", "geneList", "NCG_EXTID2PATHID", "NCG_PATHID2EXTID", "NCG_PATHID2NAME", "VDGN_EXTID2PATHID", "VDGN_PATHID2EXTID", "VDGN_PATHID2NAME" ] }, { "page": "dose_params", "title": "Shared parameters for DOSE functions", "topics": [ "dose_params" ] }, { "page": "doseSim", "title": "doseSim", "topics": [ "doseSim", "doSim" ] }, { "page": "enrichDGN", "title": "Enrichment analysis based on the DisGeNET ()", "topics": [ "enrichDGN" ] }, { "page": "enrichDGNv", "title": "enrichDGN", "topics": [ "enrichDGNv" ] }, { "page": "enrichDO", "title": "DO Enrichment Analysis", "topics": [ "enrichDO" ] }, { "page": "enrichNCG", "title": "enrichNCG", "topics": [ "enrichNCG" ] }, { "page": "gene2DO", "title": "convert Gene ID to DO Terms", "topics": [ "gene2DO" ] }, { "page": "geneSim", "title": "geneSim", "topics": [ "geneSim" ] }, { "page": "gseDGN", "title": "DisGeNET Gene Set Enrichment Analysis", "topics": [ "gseDGN" ] }, { "page": "gseDO", "title": "DO Gene Set Enrichment Analysis", "topics": [ "gseDO" ] }, { "page": "gseNCG", "title": "NCG Gene Set Enrichment Analysis", "topics": [ "gseNCG" ] }, { "page": "mclusterSim", "title": "mclusterSim", "topics": [ "mclusterSim" ] }, { "page": "simplot", "title": "simplot", "topics": [ "simplot" ] }, { "page": "theme_dose", "title": "theme_dose", "topics": [ "theme_dose" ] } ], "_readme": "https://github.com/bioc/DOSE/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "digest", "enrichit", "farver", "fastmap", "fs", "generics", "ggplot2", "glue", "GO.db", "GOSemSim", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pkgconfig", "plyr", "png", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "sys", "vctrs", "viridisLite", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "DOSE.Rmd", "filename": "DOSE.html", "title": "DOSE: Disease Ontology Semantic and Enrichment analysis", "author": "Guangchuang Yu", "engine": "knitr::rmarkdown", "headings": [ "Vignette", "Citation", "Need helps?" ], "created": "2015-06-24 07:20:05", "modified": "2020-09-09 02:50:15", "commits": 23 } ], "_score": 15.241280887440606, "_indexed": true, "_nocasepkg": "dose", "_universes": [ "bioc", "guangchuangyu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.7.0", "date": "2026-05-29T10:34:50.000Z", "distro": "noble", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "fd599e2eca94adfd95502efc12797c95bb9cc13d8831eed48e065aa2f4922d7e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.6.0", "os": "linux", "version": "4.7.0", "date": "2026-05-29T10:34:43.000Z", "distro": "noble", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "aaeb202de47a451f3a66e4fd8dcbd05e88e02ed30d80ad6d40d034fbdf877af2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.5.3", "os": "mac", "version": "4.7.0", "date": "2026-05-29T12:11:45.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "e383ccc038a4b40f82f73af151432d64f4502e662351a5a63aee2ba6f851bfed", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.6.0", "os": "mac", "version": "4.7.0", "date": "2026-05-29T12:12:03.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "d0acf4127b07b899946a62a6329f67dee6707ffd817e2ddba48f550d5bcd3597", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.6.0", "os": "wasm", "version": "4.7.0", "date": "2026-05-29T10:34:09.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "94dc0149d388c8dfb2b6a7b45a015f31f38f6036dbeec64f2dbe30903afa80b8", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.7.0", "os": "win", "version": "4.7.0", "date": "2026-05-29T10:33:13.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "a3d5a572e13326efc61669ee8082c120b581283c5f9bf25be21a8c6877f5c078", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.5.3", "os": "win", "version": "4.7.0", "date": "2026-05-29T10:33:05.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "1ad0b712a8d03a7123494097adab7e557f31a82b73c0072859d2792a1a54245a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" }, { "r": "4.6.0", "os": "win", "version": "4.7.0", "date": "2026-05-29T10:35:24.000Z", "commit": "0f4f367d08fca8f978ace7ccf3b6fc12379205df", "fileid": "a65c6402ec3f8c1641d103931f71d229ec5407c0701318f3352f2e9d9d02b788", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26632069439" } ] }