{
  "_id": "6ae73bcb9ceaa78f20099a2b",
  "Package": "DOSE",
  "Type": "Package",
  "Title": "Disease Ontology Semantic and Enrichment analysis",
  "Version": "4.7.3",
  "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 <guangchuangyu@gmail.com>",
  "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": "2026-11-01 12:53:40 UTC",
    "User": "root"
  },
  "biocViews": "Annotation, Visualization, MultipleComparison,\nGeneSetEnrichment, Pathways, Software",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-09-24 01:21:11 UTC",
  "RemoteUrl": "https://github.com/bioc/DOSE",
  "RemoteRef": "HEAD",
  "RemoteSha": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
  "NeedsCompilation": "no",
  "Author": "Guangchuang Yu [aut, cre],\nLi-Gen Wang [ctb],\nVladislav Petyuk [ctb],\nGiovanni Dall'Olio [ctb]",
  "_user": "bioc",
  "_type": "src",
  "_file": "DOSE_4.7.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/706ead0161115c0b68aa4735b5240ab76712b0cc35e09c74b9c78335f097ba70",
  "_filesize": 322432,
  "_sha256": "706ead0161115c0b68aa4735b5240ab76712b0cc35e09c74b9c78335f097ba70",
  "_expires": "2027-02-09T13:16:58.000Z",
  "_created": "2026-11-01T12:53:40.000Z",
  "_published": "2026-11-01T13:16:59.809Z",
  "_upstream": "https://github.com/bioc/DOSE",
  "_status": "success",
  "_maintainer": {
    "name": "Guangchuang Yu",
    "email": "guangchuangyu@gmail.com",
    "login": "guangchuangyu",
    "twitter": "@guangchuangyu",
    "description": "Professor of Bioinformatics at Southern Medical University.",
    "uuid": 626539
  },
  "_jobs": [
    {
      "job": 124854293823,
      "time": 204,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13084810835"
    },
    {
      "job": 124854293884,
      "time": 395,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13084921044"
    },
    {
      "job": 124854293924,
      "time": 374,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13084950950"
    },
    {
      "job": 124854293889,
      "time": 275,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13084672456"
    },
    {
      "job": 124854293853,
      "time": 253,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13085081504"
    },
    {
      "job": 124853119344,
      "time": 307,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13084825053"
    },
    {
      "job": 124854293888,
      "time": 180,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13084985338"
    },
    {
      "job": 124854293990,
      "time": 233,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13084751212"
    },
    {
      "job": 124854293860,
      "time": 256,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13084129092"
    },
    {
      "job": 124854293847,
      "time": 247,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13084701751"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650",
  "_commit": {
    "id": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
    "author": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "committer": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "message": "fixed r check\n",
    "time": 1790212871
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "enrichit",
      "version": ">= 0.2.2",
      "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": "aisdk",
      "role": "Suggests"
    },
    {
      "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": 80,
  "_updates": [
    {
      "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
    },
    {
      "week": "2026-30",
      "n": 6
    },
    {
      "week": "2026-31",
      "n": 3
    },
    {
      "week": "2026-38",
      "n": 2
    },
    {
      "week": "2026-39",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "4.7.3",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "4.6.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "annotation",
    "visualization",
    "multiplecomparison",
    "genesetenrichment",
    "pathways",
    "software",
    "disease-ontology",
    "enrichment-analysis",
    "semantic-similarity",
    "quarto"
  ],
  "_stars": 125,
  "_contributors": [
    {
      "user": "guangchuangyu",
      "count": 895,
      "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": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 59477,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DOSE"
  },
  "_mentions": 138,
  "_devurl": "https://github.com/guangchuangyu/dose",
  "_searchresults": 3408,
  "_quarto": true,
  "_abi": {
    "exports": [
      {
        "key": "DOSE::doseInterpretResult",
        "hash": "897d2fd70667b5bf"
      },
      {
        "key": "DOSE::generic:evidence",
        "hash": "9637e3f1eb955e19"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DOSE.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/yulab-smu/dose",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "as.data.frame",
    "clusterSim",
    "doseInterpretResult",
    "doseSim",
    "doSim",
    "enrichDO",
    "enrichNCG",
    "evidence",
    "explainDisease",
    "facet_grid",
    "gene2DO",
    "geneSim",
    "get_organism",
    "gseDO",
    "gseNCG",
    "interpretDisease",
    "mclusterSim",
    "rankMouseModels",
    "set_auto_update",
    "show",
    "simplot",
    "summary",
    "theme_dose"
  ],
  "_datasets": [
    {
      "name": "geneList",
      "title": "Datasets",
      "object": "geneList",
      "file": "geneList.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "doseInterpretResult-dataframe",
      "title": "Coerce a canonical interpretation result to a data.frame",
      "topics": [
        "as.data.frame,doseInterpretResult-method"
      ]
    },
    {
      "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": "doseInterpretResult",
      "title": "Construct a canonical interpretation result",
      "topics": [
        "doseInterpretResult"
      ]
    },
    {
      "page": "doseInterpretResult-class",
      "title": "Canonical interpretation result class",
      "topics": [
        "doseInterpretResult-class"
      ]
    },
    {
      "page": "doseSim",
      "title": "doseSim",
      "topics": [
        "doseSim",
        "doSim"
      ]
    },
    {
      "page": "enrichDO",
      "title": "DO Enrichment Analysis",
      "topics": [
        "enrichDO"
      ]
    },
    {
      "page": "enrichNCG",
      "title": "enrichNCG",
      "topics": [
        "enrichNCG"
      ]
    },
    {
      "page": "evidence",
      "title": "Filter evidence rows from a canonical interpretation result",
      "topics": [
        "evidence",
        "evidence,doseInterpretResult-method"
      ]
    },
    {
      "page": "explainDisease",
      "title": "Add evidence-grounded explanation text to a canonical interpretation result",
      "topics": [
        "explainDisease"
      ]
    },
    {
      "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": "interpretDisease",
      "title": "High-level disease interpretation entry point",
      "topics": [
        "interpretDisease"
      ]
    },
    {
      "page": "mclusterSim",
      "title": "mclusterSim",
      "topics": [
        "mclusterSim"
      ]
    },
    {
      "page": "rankMouseModels",
      "title": "Rank mouse disease models from human query genes",
      "topics": [
        "rankMouseModels"
      ]
    },
    {
      "page": "doseInterpretResult-show",
      "title": "Show a canonical interpretation result",
      "topics": [
        "show,doseInterpretResult-method"
      ]
    },
    {
      "page": "simplot",
      "title": "simplot",
      "topics": [
        "simplot"
      ]
    },
    {
      "page": "doseInterpretResult-summary",
      "title": "Summarize a canonical interpretation result",
      "topics": [
        "summary,doseInterpretResult-method"
      ]
    },
    {
      "page": "theme_dose",
      "title": "theme_dose",
      "topics": [
        "theme_dose"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DOSE/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "digest",
    "enrichit",
    "farver",
    "fastmap",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "GO.db",
    "GOSemSim",
    "gson",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "plyr",
    "png",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "reshape2",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "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": 15.7382124049875,
  "_indexed": true,
  "_nocasepkg": "dose",
  "_universes": [
    "bioc",
    "guangchuangyu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.7.3",
      "date": "2026-11-01T13:00:25.000Z",
      "distro": "resolute",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/44017fc87292106e79d120f29d42b7b03e8f1a1528a44cad26b6e2a3da744db2",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "4.7.3",
      "date": "2026-11-01T13:00:09.000Z",
      "distro": "resolute",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/68e0ce5569121343dfd7f4d2185de8d5d17d93ae3b5c8c5ff27276296ebe4446",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.7.3",
      "date": "2026-11-01T13:08:27.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/9b612219ea6b9ac89b00afa01005bf2e244930980eea16603efa6b161a28db26",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "4.7.3",
      "date": "2026-11-01T13:06:55.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/8b8f10523581e46f392524282f3d50121d7269380f29a9ff224bd06d36b1d24e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.7.3",
      "date": "2026-11-01T12:58:44.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/013543930b4b1c09ee66031c6b6cf3ad0c9c3382a02b84c8ca02faa93d397f11",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.7.3",
      "date": "2026-11-01T12:57:52.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/e77f0c00971e3c97ff8cc2a522b366bb2bb00a695e85ad7e209b23494733cb3d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "4.7.3",
      "date": "2026-11-01T12:58:03.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/36b96de9c7adcd23da4f9417efdc619f7ef58dae6dd4d4c72f91fe6c25d0f045",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "4.7.3",
      "date": "2026-11-01T12:57:54.000Z",
      "commit": "5846d72fe047f1de66d506a21c117d400e4a3ef8",
      "fileid": "https://r2.ropensci.org/f22992816f162882185a410fda23a1fea668504cc9f313b18d7ca7179081913b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308256650"
    }
  ]
}