{ "_id": "6a57f3e4ff0138dec5d722ee", "Package": "DOSE", "Type": "Package", "Title": "Disease Ontology Semantic and Enrichment analysis", "Version": "4.7.2", "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": "Provides ontology-aware methods for disease and phenotype\nknowledge mining. DOSE supports semantic similarity analysis of\ndisease and phenotype ontology terms, genes, and gene clusters\nusing methods including Resnik, Schlicker, Jiang, Lin, and\nWang. It also provides over-representation analysis and gene\nset enrichment analysis for interpreting gene vectors and\nranked gene lists in disease, phenotype, and cancer contexts.", "VignetteBuilder": "quarto", "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": "2026-07-15 20:48:46 UTC", "User": "root" }, "biocViews": "Annotation, Visualization, MultipleComparison,\nGeneSetEnrichment, Pathways, Software", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-15 15:10:22 UTC", "RemoteUrl": "https://github.com/bioc/DOSE", "RemoteRef": "HEAD", "RemoteSha": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "NeedsCompilation": "no", "Author": "Guangchuang Yu [aut, cre],\nLi-Gen Wang [ctb],\nVladislav Petyuk [ctb],\nGiovanni Dall'Olio [ctb]", "_user": "bioc", "_type": "src", "_file": "DOSE_4.7.2.tar.gz", "_fileid": "https://r2.ropensci.org/9030afc4a1b560362b19d9ed98728531e858a2c55d9f2dede6fedc440280baa7", "_filesize": 279969, "_sha256": "9030afc4a1b560362b19d9ed98728531e858a2c55d9f2dede6fedc440280baa7", "_expires": "2026-10-23T20:56:01.000Z", "_created": "2026-07-15T20:48:46.000Z", "_published": "2026-07-15T20:56:03.664Z", "_bioccheck": { "error": 1, "warning": 4, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867", "_status": "success", "_upstream": "https://github.com/bioc/DOSE", "_commit": { "id": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "author": "Guangchuang Yu ", "committer": "Guangchuang Yu ", "message": "v4.7.2\n", "time": 1784128222 }, "_maintainer": { "name": "Guangchuang Yu", "email": "guangchuangyu@gmail.com", "login": "guangchuangyu", "twitter": "@guangchuangyu", "description": "Professor of Bioinformatics at Southern Medical University.", "uuid": 626539 }, "_distro": "resolute", "_jobs": [ { "job": 87468967887, "time": 269, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8357060598" }, { "job": 87468967905, "time": 388, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8357107574" }, { "job": 87468967902, "time": 338, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8357088247" }, { "job": 87468967889, "time": 263, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8357058297" }, { "job": 87468967914, "time": 201, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8357034535" }, { "job": 87467870358, "time": 326, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8356951856" }, { "job": 87468967869, "time": 223, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8357042651" }, { "job": 87468967890, "time": 249, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8357053306" }, { "job": 87468967903, "time": 245, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8357052310" }, { "job": 87468967923, "time": 268, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8357060589" } ], "_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": ">= 2.39.2", "role": "Imports" }, { "package": "gson", "version": ">= 0.0.5", "role": "Imports" }, { "package": "memoise", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "yulab.utils", "version": "> 0.2.2", "role": "Imports" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 64, "_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": 3 }, { "week": "2026-27", "n": 7 }, { "week": "2026-29", "n": 3 } ], "_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", "quarto" ], "_stars": 125, "_contributors": [ { "user": "guangchuangyu", "count": 876, "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", "followers": 447, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 45022, "source": "https://www.bioconductor.org/packages/stats/bioc/DOSE" }, "_mentions": 138, "_devurl": "https://github.com/guangchuangyu/dose", "_searchresults": 3184, "_quarto": true, "_rbuild": "4.6.1", "_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", "enrichDO", "enrichNCG", "facet_grid", "gene2DO", "geneSim", "get_organism", "gseDO", "gseNCG", "mclusterSim", "set_auto_update", "simplot", "theme_dose" ], "_datasets": [ { "name": "geneList", "title": "Datasets", "object": "geneList", "file": "geneList.rda", "class": [ "numeric" ], "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", "geneList" ] }, { "page": "dose_params", "title": "Shared parameters for DOSE functions", "topics": [ "dose_params" ] }, { "page": "doseSim", "title": "doseSim", "topics": [ "doseSim", "doSim" ] }, { "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": "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", "dplyr", "enrichit", "farver", "fastmap", "fs", "generics", "ggplot2", "glue", "GO.db", "GOSemSim", "gson", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "reshape2", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "DOSE.qmd", "filename": "DOSE.html", "title": "DOSE", "engine": "quarto::html", "headings": [ "Overview", "Data", "Methods", "Documentation", "Citation", "Support" ], "created": "2026-06-30 05:21:56", "modified": "2026-06-30 05:21:56", "commits": 1 } ], "_score": 15.365912857246354, "_indexed": true, "_nocasepkg": "dose", "_universes": [ "bioc", "guangchuangyu" ], "_previous": "4.7.1", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.7.2", "date": "2026-07-15T20:53:46.000Z", "distro": "resolute", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/16e55b1a30a86854b6c4b729150986e536d8b52d7e6bd91e3e7672e03237d27b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.6.1", "os": "linux", "version": "4.7.2", "date": "2026-07-15T20:53:04.000Z", "distro": "resolute", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/7001bfff4baa8de7e07325d833582e5a8fa4b66cda55ef16f5cf5f417e535cff", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.5.3", "os": "mac", "version": "4.7.2", "date": "2026-07-15T20:52:14.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/83fdc2b0c28e20ee0c47b2e740c05a3a050a642404efd18b2eaf5db7b3da17d3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.6.1", "os": "mac", "version": "4.7.2", "date": "2026-07-15T20:51:29.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/52cee348c286aed054981ba2011ecc82d93ffc6bb23b9bcdf69716e45beb8504", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.6.0", "os": "wasm", "version": "4.7.2", "date": "2026-07-15T20:52:54.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/9677a7a2e35d7dc5079ecf08343876f7a12f684e83e4481c40c0e1dc56686dfb", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.7.0", "os": "win", "version": "4.7.2", "date": "2026-07-15T20:51:31.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/1e65223f7871441f402fc3367460b7a0301dbf8272758e1fcf41e3865a76f9b8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.5.3", "os": "win", "version": "4.7.2", "date": "2026-07-15T20:51:33.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/063f46f3b6f65332ccb7f0d86662b502aec7ce80f8bf4ee924a9ec850897cd46", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" }, { "r": "4.6.1", "os": "win", "version": "4.7.2", "date": "2026-07-15T20:51:45.000Z", "commit": "43eb856d5f4d360c0141b54cf5fc5a13564628f2", "fileid": "https://r2.ropensci.org/fe7ce75548990bc4df57e69bbb76ad15f406250c70a74d2851428720a9b02a0f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449375867" } ] }