{
  "_id": "6a494a88f6c47c4419498b77",
  "Package": "BiocSet",
  "Title": "Representing Different Biological Sets",
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  "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": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:26 UTC",
  "RemoteUrl": "https://github.com/bioc/BiocSet",
  "RemoteRef": "HEAD",
  "RemoteSha": "edc80df2f76a8f9674bc280de749d2c2a4289a69",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 16:21:54 UTC",
    "User": "root"
  },
  "Author": "Kayla Morrell [aut, cre],\nMartin Morgan [aut],\nKevin Rue-Albrecht [ctb],\nLluís Revilla Sancho [ctb]",
  "Maintainer": "Kayla Morrell <kayla.morrell16@gmail.com>",
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  "_type": "src",
  "_file": "BiocSet_1.27.0.tar.gz",
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  "_expires": "2026-10-12T18:01:42.000Z",
  "_created": "2026-07-03T16:21:54.000Z",
  "_published": "2026-07-04T18:01:44.433Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 9
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28672146897",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "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. ",
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  "_dependencies": [
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      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
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      "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"
    },
    {
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      "role": "Suggests"
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      "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"
    }
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.25.0",
      "bioc": "3.23"
    }
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    "geneexpression",
    "go",
    "kegg",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 34,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BiocSet.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_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"
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    },
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      "title": "OBOSet class",
      "topics": [
        "OBOSet",
        "OBOSet-class"
      ]
    },
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      "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"
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    },
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      "title": "Union on a single 'BiocSet' object",
      "topics": [
        "union_single"
      ]
    },
    {
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        "url_ref_element",
        "url_ref_set"
      ]
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