{ "_id": "6a1f1b46b401979e7341f405", "Package": "EnrichDO", "Type": "Package", "Title": "a Global Weighted Model for Disease Ontology Enrichment Analysis", "Version": "1.7.0", "Authors@R": "c(\nperson(\"Liang\", \"Cheng\", email = \"liangcheng@hrbmu.edu.cn\", role = \"aut\"),\nperson(\"Haixiu\", \"Yang\", email = \"yanghaixiu@ems.hrbmu.edu.cn\", role = \"aut\"),\nperson(\"Hongyu\", \"Fu\", email = \"2287531995@qq.com\", role = c(\"aut\", \"cre\"))\n)", "Description": "To implement disease ontology (DO) enrichment analysis,\nthis package is designed and presents a double weighted model\nbased on the latest annotations of the human genome with DO\nterms, by integrating the DO graph topology on a global scale.\nThis package exhibits high accuracy that it can identify more\nspecific DO terms, which alleviates the over enriched problem.\nThe package includes various statistical models and\nvisualization schemes for discovering the associations between\ngenes and diseases from biological big data.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Annotation, Visualization, GeneSetEnrichment, Software", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-16 09:20:32 UTC", "User": "root" }, "Author": "Liang Cheng [aut], Haixiu Yang [aut], Hongyu Fu [aut, cre]", "Maintainer": "Hongyu Fu <2287531995@qq.com>", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:40 UTC", "RemoteUrl": "https://github.com/bioc/EnrichDO", "RemoteRef": "HEAD", "RemoteSha": "e8010f257545f76527c29cb3cfc015ec36bc9389", "MD5sum": "3aafc11cef2f03fa935fdd70438039a2", "_user": "bioc", "_type": "src", "_file": "EnrichDO_1.7.0.tar.gz", "_fileid": "3e6ffd767cfadb62669c3ace590c0c8eeebfc8a1fa26428bd64671f43d12b8fb", "_filesize": 4001829, "_sha256": "3e6ffd767cfadb62669c3ace590c0c8eeebfc8a1fa26428bd64671f43d12b8fb", "_created": "2026-05-16T09:20:32.000Z", "_published": "2026-06-02T18:04:54.656Z", "_jobs": [ { "job": 79138855449, "time": 157, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7032278283" }, { "job": 79138855218, "time": 374, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7032298995" }, { "job": 79138855040, "time": 354, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7032297206" }, { "job": 79138855267, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7032282354" }, { "job": 79138855045, "time": 284, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7032290121" }, { "job": 79138854325, "time": 238, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7032263262" }, { "job": 79138854061, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7365930984" }, { "job": 79138854754, "time": 280, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7032289880" }, { "job": 79138855069, "time": 240, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7032286234" }, { "job": 79138855034, "time": 250, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7032287140" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/EnrichDO", "_commit": { "id": "e8010f257545f76527c29cb3cfc015ec36bc9389", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381420 }, "_maintainer": { "name": "Hongyu Fu", "email": "2287531995@qq.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "hash", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 14 }, { "week": "2026-14", "n": 4 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.7.0", "bioc": "3.24" }, { "branch": "release", "version": "1.6.0", "bioc": "3.23" } ], "_topics": [ "annotation", "visualization", "genesetenrichment", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 258, "source": "https://www.bioconductor.org/packages/stats/bioc/EnrichDO" }, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EnrichDO.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "0.1-1", "date": "2024-09-19" } ], "_exports": [ "convDraw", "doEnrich", "drawBarGraph", "drawGraphViz", "drawHeatmap", "drawPointGraph", "show", "showDoTerms", "viewDetailResult", "viewSummaryResult", "writeResult" ], "_datasets": [ { "name": "dotermgenes", "title": "All DO term annotated genes.", "object": "dotermgenes", "file": "dotermgenes.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "doterms", "title": "Detailed annotation information for 4831 DO terms.", "object": "doterms", "file": "doterms.rda", "class": [ "data.frame" ], "fields": [ "DOID", "level", "gene.arr", "weight.arr", "parent.arr", "parent.len", "child.arr", "child.len", "gene.len", "DOTerm" ], "rows": 4813, "table": true, "tojson": true } ], "_help": [ { "page": "EnrichDO-package", "title": "EnrichDO Enrichment analyses including a variety of statistical models and visualization schemes for discovering the disease-gene relationship under biological big data.", "topics": [ "EnrichDO-package", "EnrichDO" ] }, { "page": "convDraw", "title": "convDraw", "topics": [ "convDraw" ] }, { "page": "doEnrich", "title": "doEnrich", "topics": [ "doEnrich" ] }, { "page": "dotermgenes", "title": "All DO term annotated genes.", "topics": [ "dotermgenes" ] }, { "page": "doterms", "title": "Detailed annotation information for 4831 DO terms.", "topics": [ "doterms" ] }, { "page": "drawBarGraph", "title": "drawBarGraph", "topics": [ "drawBarGraph" ] }, { "page": "drawGraphViz", "title": "drawGraphViz", "topics": [ "drawGraphViz" ] }, { "page": "drawHeatmap", "title": "drawHeatmap", "topics": [ "drawHeatmap" ] }, { "page": "drawPointGraph", "title": "drawPointGraph", "topics": [ "drawPointGraph" ] }, { "page": "EnrichResult-class", "title": "Class 'EnrichResult' This class represents the result of enrich analysis", "topics": [ "EnrichResult-class" ] }, { "page": "show-methods", "title": "show method", "topics": [ "show,EnrichResult-method" ] }, { "page": "showDoTerms", "title": "showDoTerms", "topics": [ "showDoTerms" ] }, { "page": "TermStruct", "title": "Enrich_internal", "topics": [ "TermStruct" ] }, { "page": "viewDetailResult", "title": "viewDetailResult method", "topics": [ "viewDetailResult", "viewDetailResult,EnrichResult-method" ] }, { "page": "viewSummaryResult", "title": "viewSummaryResult method", "topics": [ "viewSummaryResult", "viewSummaryResult,EnrichResult-method" ] }, { "page": "writeResult", "title": "writeResult", "topics": [ "writeResult" ] } ], "_readme": "https://github.com/bioc/EnrichDO/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "graph", "gtable", "hash", "isoband", "labeling", "lifecycle", "magrittr", "pheatmap", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rgraphviz", "rlang", "S4Vectors", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "EnrichDO.Rmd", "filename": "EnrichDO.html", "title": "EnrichDO: a Global Weighted Model for Disease Ontology Enrichment Analysis", "author": "Liang Cheng, Haixiu Yang, Hongyu Fu", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Citation", "Introduction", "Disease Ontology Enrichment Analysis", "Data Preparation", "doEnrich Function", "Weighted Enrichment Function", "Classic Enrichment Function", "Result description and Written", "Enrichment description", "Result Display", "Result writing", "Visualization of enrichment results", "drawBarGraph function", "drawPointGraph function", "drawGraphViz function", "drawHeatmap function", "convenient drawing", "Session information" ], "created": "2024-06-07 07:45:46", "modified": "2026-03-31 14:42:18", "commits": 15 } ], "_score": 4.217483944213907, "_indexed": true, "_nocasepkg": "enrichdo", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.0", "date": "2026-05-16T09:23:58.000Z", "distro": "noble", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "46713fcab224d4eb19a2be939a71b86c8252fb5e415e128ee005f005b73de836", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.6.0", "os": "linux", "version": "1.7.0", "date": "2026-05-16T09:23:46.000Z", "distro": "noble", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "505779a3d970474f9e4fc5d993a9b703ed467e8926138c26ee883895967cc71a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0", "date": "2026-05-16T09:22:17.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "894fff2ce67e0a6360a2db6981de895f3035459283798a040e3593bb01b15745", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.6.0", "os": "mac", "version": "1.7.0", "date": "2026-05-16T09:22:22.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "102c219e27acbceeb7ed9ac4de6ba9dc667c2fd830e10a8c561fdafa26558a2f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.7.0", "os": "win", "version": "1.7.0", "date": "2026-05-16T09:22:08.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "2f841933999c94f68bdd3e513aa9c8f9069fc841c72d347855606b45fdbf2cff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.5.3", "os": "win", "version": "1.7.0", "date": "2026-05-16T09:21:53.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "b5dc68853f8d06c7fe4eb9aea70df4cc798173aeb9442433e64adc7adec3ea3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.6.0", "os": "win", "version": "1.7.0", "date": "2026-05-16T09:21:52.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "0d6e7667328daa128c769b0f51f673f69600b349e7e93b9c3ecc397dde6c542b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.0", "date": "2026-06-02T18:04:31.000Z", "commit": "e8010f257545f76527c29cb3cfc015ec36bc9389", "fileid": "b33b25e879b166011e75858effccec51a725cb1675f65cce06e07d7fe4220306", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25958243061" } ] }