{ "_id": "6ad33dc690c8bbdf41a51888", "Package": "BiocSet", "Title": "Representing Different Biological Sets", "Version": "1.26.0", "Authors@R": "c(\nperson(\"Kayla\", \"Morrell\", email = \"kayla.morrell16@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Martin\", \"Morgan\", role = \"aut\"),\nperson(\"Kevin\", \"Rue-Albrecht\", role = \"ctb\"),\nperson(\"Lluís\", \"Revilla Sancho\", role = \"ctb\"))", "Description": "BiocSet displays different biological sets in a triple\ntibble format. These three tibbles are `element`, `set`, and\n`elementset`. The user has the abilty to activate one of these\nthree tibbles to perform common functions from the dplyr\npackage. Mapping functionality and accessing web references for\nelements/sets are also available in BiocSet.", "biocViews": "GeneExpression, GO, KEGG, Software", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:51:26 UTC", "RemoteUrl": "https://github.com/bioc/BiocSet", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-17 09:10:57 UTC", "User": "root" }, "Author": "Kayla Morrell [aut, cre],\nMartin Morgan [aut],\nKevin Rue-Albrecht [ctb],\nLluís Revilla Sancho [ctb]", "Maintainer": "Kayla Morrell ", "_user": "bioc-release", "_type": "src", "_file": "BiocSet_1.26.0.tar.gz", "_fileid": "https://r2.ropensci.org/cec41b36ddde70a229424250f6862265b929708089d70005f880277867e9de72", "_filesize": 177569, "_sha256": "cec41b36ddde70a229424250f6862265b929708089d70005f880277867e9de72", "_expires": "2027-01-25T09:20:04.000Z", "_created": "2026-10-17T09:10:57.000Z", "_published": "2026-10-17T09:20:06.263Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 2, "note": 10 }, "_upstream": "https://github.com/bioc/BiocSet", "_commit": { "id": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380686 }, "_maintainer": { "name": "Kayla Morrell", "email": "kayla.morrell16@gmail.com", "login": "kayla-morrell", "twitter": "@kaylainter1011", "description": "Core team member of Bioconductor at Roswell Park Comprehensive Cancer Center. R 📦 development, support, and maintenance. ", "uuid": 32339524 }, "_distro": "resolute", "_jobs": [ { "job": 117360264110, "time": 207, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12096616980" }, { "job": 117360264042, "time": 329, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12096701513" }, { "job": 117360264106, "time": 364, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12096527587" }, { "job": 117360264040, "time": 224, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "12096592607" }, { "job": 117360264049, "time": 244, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12096915130" }, { "job": 117359359144, "time": 302, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "12096203181" }, { "job": 117360264036, "time": 163, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12096044164" }, { "job": 117360264038, "time": 188, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12095994592" }, { "job": 117360264093, "time": 220, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "12096128780" }, { "job": 117360264094, "time": 244, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12096089170" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "dplyr", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "BiocIO", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "KEGGREST", "role": "Imports" }, { "package": "ontologyIndex", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "GSEABase", "role": "Suggests" }, { "package": "airway", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "GO.db", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 3, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.25.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "geneexpression", "go", "kegg", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 772, "source": "https://www.bioconductor.org/packages/stats/bioc/BiocSet" }, "_searchresults": 40, "_rbuild": "4.6.1", "_assets": [ "extra/BiocSet.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "arrange_element", "arrange_elementset", "arrange_set", "BiocSet", "BiocSet_from_elementset", "BiocSet_from_GeneSetCollection", "coerce", "data.frame_from_element", "data.frame_from_elementset", "data.frame_from_set", "es_activate", "es_element", "es_elementset", "es_set", "export", "filter_element", "filter_elementset", "filter_set", "GeneSetCollection_from_BiocSet", "go_sets", "import", "intersect_single", "kegg_sets", "left_join_element", "left_join_elementset", "left_join_set", "map_add_element", "map_add_set", "map_multiple", "map_set", "map_unique", "metadata", "metadata<-", "mutate_element", "mutate_elementset", "mutate_set", "OBOSet", "oboset_element_ancestors", "oboset_element_children", "oboset_element_parents", "oboset_set_ancestors", "oboset_set_children", "oboset_set_parents", "select_element", "select_elementset", "select_set", "summarise_element", "summarise_elementset", "summarise_set", "tibble_from_element", "tibble_from_elementset", "tibble_from_set", "union_single", "url_ref", "url_ref_element", "url_ref_set" ], "_help": [ { "page": "BiocSet-class", "title": "BiocSet class", "topics": [ "BiocSet", "BiocSet-class", "BiocSet_from_elementset", "es_element", "es_element,BiocSet-method", "es_elementset", "es_elementset,BiocSet-method", "es_set", "es_set,BiocSet-method", "show,BiocSet-method" ] }, { "page": "coerce", "title": "as(\"BiocSet\", \"list\")", "topics": [ "coerce", "coerce,BiocSet,list-method" ] }, { "page": "element_funs", "title": "Functions applied to elements in a 'BiocSet' object", "topics": [ "arrange_element", "data.frame_from_element", "element_funs", "filter_element", "left_join_element", "mutate_element", "select_element", "summarise_element", "tibble_from_element" ] }, { "page": "elementset_funs", "title": "Functions applied to elementsets in a 'BiocSet' object", "topics": [ "arrange_elementset", "data.frame_from_elementset", "elementset_funs", "filter_elementset", "left_join_elementset", "mutate_elementset", "select_elementset", "summarise_elementset", "tibble_from_elementset" ] }, { "page": "genesetcollection", "title": "GeneSetCollection", "topics": [ "BiocSet_from_GeneSetCollection", "genesetcollection", "GeneSetCollection_from_BiocSet" ] }, { "page": "import", "title": "Importing/exporting", "topics": [ "export,BiocSet,GMTFile,ANY-method", "export,BiocSet,OBOFile,ANY-method", "import", "import,GMTFile,ANY,ANY-method", "import,OBOFile,ANY,ANY-method" ] }, { "page": "intersect_single", "title": "Intersect on a single 'BiocSet' object", "topics": [ "intersect_single" ] }, { "page": "mapping_element", "title": "Functions for mapping elements in the element tibble to different id types", "topics": [ "mapping_element", "map_add_element", "map_multiple", "map_unique" ] }, { "page": "mapping_set", "title": "Functions for mapping sets in the set tibble to different id types", "topics": [ "go_sets", "kegg_sets", "mapping_set", "map_add_set", "map_set" ] }, { "page": "obo_relations", "title": "Functions to display relationships of an 'OBOSet' object", "topics": [ "oboset_element_ancestors", "oboset_element_children", "oboset_element_parents", "oboset_set_ancestors", "oboset_set_children", "oboset_set_parents", "obo_relations" ] }, { "page": "OBOSet-class", "title": "OBOSet class", "topics": [ "OBOSet", "OBOSet-class" ] }, { "page": "set_funs", "title": "Functions applied to sets in a 'BiocSet' object", "topics": [ "arrange_set", "data.frame_from_set", "filter_set", "left_join_set", "mutate_set", "select_set", "set_funs", "summarise_set", "tibble_from_set" ] }, { "page": "union_single", "title": "Union on a single 'BiocSet' object", "topics": [ "union_single" ] }, { "page": "url_ref", "title": "Functions to access reference urls for different identifiers", "topics": [ "url_ref", "url_ref_element", "url_ref_set" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "BiocIO", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dplyr", "fastmap", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "ontologyIndex", "openssl", "pillar", "pkgconfig", "plyr", "png", "purrr", "R6", "Rcpp", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_score": 3.8573324964312685, "_indexed": false, "_nocasepkg": "biocset", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/BiocSet", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-10-17T09:14:57.000Z", "distro": "resolute", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/a56b11ffd2b0fe5fb4f480b825ebbc9b4c5f29e86630cba41230d086329ce889", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.6.1", "os": "linux", "version": "1.26.0", "date": "2026-10-17T09:15:55.000Z", "distro": "resolute", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/81001892c21f1504c9aad03a37f74254f886972feb48ca06737a5416ee616e8a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.5.3", "os": "mac", "version": "1.26.0", "date": "2026-10-17T09:17:39.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/ef86fc973e8ba7f53bcf68cfab37ccc80e191075bb3dba5fa8c96ba63eaf8741", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.6.1", "os": "mac", "version": "1.26.0", "date": "2026-10-17T09:17:36.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/2be941bc74228fb0244797435539cd32e545d75deb3a33335c2925ebc2f6799f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.6.0", "os": "wasm", "version": "1.26.0", "date": "2026-10-17T09:14:12.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/bb0b20ffa8500d4f6ce9d81ba1932c4a7f5b41fa07f284fa46d1afbfe6262ae3", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.7.0", "os": "win", "version": "1.26.0", "date": "2026-10-17T09:13:06.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/b5090024cdbef31b14410c98e59cd626cdfc754799b7c715243ef8a59611c8a7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.5.3", "os": "win", "version": "1.26.0", "date": "2026-10-17T09:13:06.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/810ce5fbb0c2a110054f1848951d2cc44c5ffe479cf9aa36a2b36bede04397c0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" }, { "r": "4.6.1", "os": "win", "version": "1.26.0", "date": "2026-10-17T09:13:26.000Z", "commit": "f83c337e7da7be859f9d146daaa227ddff5f7efa", "fileid": "https://r2.ropensci.org/c7d559c13367c8c46f0411bfb33b72bd608d2162c3f704742f63cae577499dae", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39019844995" } ] }