{ "_id": "6a49b0e0c8f6781c04fb8ab4", "Package": "geneset", "Type": "Package", "Title": "Get Gene Sets for Gene Enrichment Analysis", "Version": "0.2.8", "Authors@R": "c(person(given = \"Yunze\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jieandze1314@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7414-8556\")))", "Maintainer": "Yunze Liu ", "URL": "https://github.com/GangLiLab/geneset", "BugReports": "https://github.com/GangLiLab/geneset/issues", "Description": "Gene sets are fundamental for gene enrichment analysis.\nThe package 'geneset' enables querying gene sets from public\ndatabases including 'GO' (Gene Ontology Consortium. (2004)\n), 'KEGG' (Minoru et al. (2000)\n), 'WikiPathway' (Marvin et al. (2020)\n), 'MsigDb' (Arthur et al. (2015)\n), 'Reactome' (David et al.\n(2011) ), 'MeSH' (Ish et al. (2014)\n), 'DisGeNET' (Janet et al.\n(2017) ), 'Disease Ontology' (Lynn et\nal. (2011) ), 'Network of Cancer Genes'\n(Dimitra et al. (2019) ) and\n'COVID-19' (Maxim et al. (2020)\n). Gene sets are stored in the\nlist object which provides data frame of 'geneset' and\n'geneset_name'. The 'geneset' has two columns of term ID and\ngene ID. The 'geneset_name' has two columns of terms ID and\nterm description.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.2", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://ganglilab.r-universe.dev", "Date/Publication": "2023-08-09 04:45:04 UTC", "RemoteUrl": "https://github.com/ganglilab/geneset", "RemoteRef": "HEAD", "RemoteSha": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-19 10:44:34 UTC", "User": "root" }, "Author": "Yunze Liu [aut, cre] (ORCID: )", "_user": "ganglilab", "_type": "src", "_file": "geneset_0.2.8.tar.gz", "_fileid": "https://r2.ropensci.org/0ecaf6067cb77d901beb8d11e7f61ba6e39438d691ab1bd167e21003df8a4665", "_filesize": 323476, "_sha256": "0ecaf6067cb77d901beb8d11e7f61ba6e39438d691ab1bd167e21003df8a4665", "_expires": "2026-10-13T01:18:23.000Z", "_created": "2026-06-19T10:44:34.000Z", "_published": "2026-07-05T01:18:24.926Z", "_jobs": [ { "job": 85181986742, "time": 159, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7747842300" }, { "job": 85181986710, "time": 124, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7747831516" }, { "job": 85181986792, "time": 146, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7747830111" }, { "job": 85181986816, "time": 120, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7747824711" }, { "job": 85181986674, "time": 211, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7747791412" }, { "job": 85181986818, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7747822720" }, { "job": 85181986754, "time": 92, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7747822529" }, { "job": 85181986916, "time": 76, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7747816156" }, { "job": 85181986767, "time": 71, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7747814923" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775", "_status": "success", "_upstream": "https://github.com/ganglilab/geneset", "_commit": { "id": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "author": "reedliu ", "committer": "reedliu ", "message": "add new file\n", "time": 1691556304 }, "_maintainer": { "name": "Yunze Liu", "email": "jieandze1314@gmail.com", "login": "reedliu", "description": "Co-founder of Bioinfoplanet “生信星球”", "uuid": 34302878, "orcid": "0000-0002-7414-8556" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "fst", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ganglilab", "_selfowned": true, "_usedby": 2, "_updates": [], "_tags": [], "_topics": [ "enrichment-analysis", "gene", "geneset-enrichment" ], "_stars": 11, "_contributors": [ { "user": "reedliu", "count": 33, "uuid": 34302878 } ], "_userbio": { "uuid": 85151598, "type": "organization", "name": "GangLi_Lab", "followers": 17, "description": "Research group led by Gang Li in University of Macau" }, "_downloads": { "count": 404, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/geneset" }, "_devurl": "https://github.com/ganglilab/geneset", "_searchresults": 47, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/geneset.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ganglilab/geneset", "_realowner": "ganglilab", "_cranurl": true, "_releases": [ { "version": "0.2.6", "date": "2022-07-18" }, { "version": "0.2.7", "date": "2022-11-20" } ], "_exports": [ "getEnrichrdb", "getGO", "getHgDisease", "getKEGG", "getMesh", "getMsigdb", "getReactome", "getWiki" ], "_datasets": [ { "name": "enrichr_metadata", "title": "Datasets go_org contains GO species information", "object": "enrichr_metadata", "class": [ "data.frame" ], "fields": [ "library", "term_number", "gene_coverage", "genes_per_term", "organism" ], "rows": 276, "table": true, "tojson": true }, { "name": "ensOrg_name", "title": "Datasets go_org contains GO species information", "object": "ensOrg_name", "class": [ "data.frame" ], "fields": [ "common_name", "latin_full_name", "latin_short_name", "bioc_name" ], "rows": 317, "table": true, "tojson": true }, { "name": "go_org", "title": "Datasets go_org contains GO species information", "object": "go_org", "class": [ "data.frame" ], "fields": [ "common_name", "latin_full_name" ], "rows": 143, "table": true, "tojson": true }, { "name": "kegg_org", "title": "Datasets go_org contains GO species information", "object": "kegg_org", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "kegg_name", "latin_full_name", "common_name" ], "rows": 8213, "table": true, "tojson": true }, { "name": "mesh_metadata", "title": "Datasets go_org contains GO species information", "object": "mesh_metadata", "class": [ "grouped_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "mesh_org", "method", "category" ], "rows": 125, "table": true, "tojson": true }, { "name": "mesh_org", "title": "Datasets go_org contains GO species information", "object": "mesh_org", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "mesh_org", "latin_full_name", "common_name" ], "rows": 71, "table": true, "tojson": true }, { "name": "msigdb_org", "title": "Datasets go_org contains GO species information", "object": "msigdb_org", "class": [ "data.frame" ], "fields": [ "latin_full_name", "common_name" ], "rows": 20, "table": true, "tojson": true }, { "name": "org2cate", "title": "Datasets go_org contains GO species information", "object": "org2cate", "class": [ "data.frame" ], "fields": [ "latin_full_name", "category" ], "rows": 8426, "table": true, "tojson": true }, { "name": "reactome_org", "title": "Datasets go_org contains GO species information", "object": "reactome_org", "class": [ "data.frame" ], "fields": [ "latin_full_name", "common_name" ], "rows": 11, "table": true, "tojson": true }, { "name": "wiki_org", "title": "Datasets go_org contains GO species information", "object": "wiki_org", "class": [ "data.frame" ], "fields": [ "common_name", "latin_full_name" ], "rows": 16, "table": true, "tojson": true } ], "_help": [ { "page": "Datasets", "title": "Datasets go_org contains GO species information", "topics": [ "Datasets", "enrichr_metadata", "ensOrg_name", "go_org", "kegg_org", "mesh_metadata", "mesh_org", "msigdb_org", "org2cate", "reactome_org", "wiki_org" ] }, { "page": "getEnrichrdb", "title": "Get EnrichrDB geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id", "topics": [ "getEnrichrdb" ] }, { "page": "getGO", "title": "Get GO geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getGO" ] }, { "page": "getHgDisease", "title": "Get HgDisease geneset and geneset_name Human disease gene sets from Disease Ontology (DO),DisGeNET, Network of Cancer Gene (NCG) version 6 and v7, and covid19-specific. Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getHgDisease" ] }, { "page": "getKEGG", "title": "Get KEGG geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getKEGG" ] }, { "page": "getMesh", "title": "Get MeSH geneset and geneset_name MeSH is the annotation used for MEDLINE/PubMed articles and is manually curated by NLM (U.S. National Library of Medicine). Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getMesh" ] }, { "page": "getMsigdb", "title": "Get MsigDb geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id", "topics": [ "getMsigdb" ] }, { "page": "getReactome", "title": "Get Reactome geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getReactome" ] }, { "page": "getWiki", "title": "Get WikiPathway geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description", "topics": [ "getWiki" ] } ], "_readme": "https://github.com/ganglilab/geneset/raw/HEAD/README.md", "_rundeps": [ "bitops", "cli", "dplyr", "fst", "fstcore", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "Rcpp", "RCurl", "rlang", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_score": 5.190611797813604, "_indexed": true, "_nocasepkg": "geneset", "_universes": [ "ganglilab", "reedliu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.8", "date": "2026-06-19T10:47:09.000Z", "distro": "noble", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/b2f8c5a9091c8221ba0b1e4a012acf8c90a3dda5213d4f264e078988a225d3cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.6.0", "os": "linux", "version": "0.2.8", "date": "2026-06-19T10:46:34.000Z", "distro": "noble", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/5e4a0749c30a8d68256d4f2dd03e948f31ef4bc4f2f1853d90791bad211efb6d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.5.3", "os": "mac", "version": "0.2.8", "date": "2026-06-19T10:46:33.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/cac38d702b4a6a0ac21aadd00511a3fead4cf8e0ff883814b3d9c80007c95284", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.6.0", "os": "mac", "version": "0.2.8", "date": "2026-06-19T10:46:20.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/3a961aeea21e9dd7020b115550a6b4db94f77da19f89f6939209040682465ef7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.8", "date": "2026-06-19T10:46:28.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/6920d5938ff46c9827015ba8267a6211181352a53e3ed8de665e8e51eec41854", "status": "success", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.7.0", "os": "win", "version": "0.2.8", "date": "2026-06-19T10:46:02.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/057bce3260ebb7d28966d91dffc98ceb6fa789e1a0015800ca8575f132232571", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.5.3", "os": "win", "version": "0.2.8", "date": "2026-06-19T10:45:43.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/c3d759a5d3ad6b3605abe1132621a5303460633e54941e81c46c21f3c64f2a60", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" }, { "r": "4.6.0", "os": "win", "version": "0.2.8", "date": "2026-06-19T10:45:39.000Z", "commit": "b5c20beeccd6b60b7a24fcda4dcdf1032fc8238d", "fileid": "https://r2.ropensci.org/90f1a717a05384f4e61419b39d85030c185673ebc0f4ac4dd288ac5efbb3536d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ganglilab/actions/runs/27820883775" } ] }