{
  "_id": "6a1b02fa1d7bb097a0a010bf",
  "Package": "rrvgo",
  "Type": "Package",
  "Title": "Reduce + Visualize GO",
  "Version": "1.24.0",
  "Authors@R": "c(person(\"Sergi\", \"Sayols\", email = \"sergisayolspuig@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Sara\", \"Elmeligy\", role = \"ctb\"))",
  "Description": "Reduce and visualize lists of Gene Ontology terms by\nidentifying redudance based on semantic similarity.",
  "URL": "https://www.bioconductor.org/packages/rrvgo,\nhttps://ssayols.github.io/rrvgo/index.html",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "biocViews": "Annotation, Clustering, GO, Network, Pathways, Software",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:56 UTC",
  "RemoteUrl": "https://github.com/bioc/rrvgo",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "831eac118ad53b61be846ef704c1c09b9cdd1568",
  "Packaged": {
    "Date": "2026-05-30 10:07:30 UTC",
    "User": "root"
  },
  "Author": "Sergi Sayols [aut, cre],\nSara Elmeligy [ctb]",
  "Maintainer": "Sergi Sayols <sergisayolspuig@gmail.com>",
  "MD5sum": "4c55b4bda83756fe445e60811fd533d1",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "rrvgo_1.24.0.tar.gz",
  "_fileid": "e4a5e81d0c25862d3e20a42fe744fbf6cd2014bcba606cb9ccdaedbd30645b4c",
  "_filesize": 1943190,
  "_sha256": "e4a5e81d0c25862d3e20a42fe744fbf6cd2014bcba606cb9ccdaedbd30645b4c",
  "_created": "2026-05-30T10:07:30.000Z",
  "_published": "2026-05-30T15:32:10.479Z",
  "_jobs": [
    {
      "job": 78641655063,
      "time": 433,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307656212"
    },
    {
      "job": 78641655064,
      "time": 1001,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307710615"
    },
    {
      "job": 78641655065,
      "time": 662,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307678310"
    },
    {
      "job": 78641655079,
      "time": 762,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309268562"
    },
    {
      "job": 78641655098,
      "time": 657,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309263189"
    },
    {
      "job": 78640275922,
      "time": 536,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307406518"
    },
    {
      "job": 78641655077,
      "time": 384,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307651430"
    },
    {
      "job": 78641655149,
      "time": 842,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307694314"
    },
    {
      "job": 78641655121,
      "time": 917,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307702015"
    },
    {
      "job": 78641655130,
      "time": 807,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307691090"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/rrvgo",
  "_commit": {
    "id": "831eac118ad53b61be846ef704c1c09b9cdd1568",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380716
  },
  "_maintainer": {
    "name": "Sergi Sayols",
    "email": "sergisayolspuig@gmail.com",
    "login": "ssayols",
    "description": "",
    "uuid": 6011316
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "GOSemSim",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "treemap",
      "role": "Imports"
    },
    {
      "package": "tm",
      "role": "Imports"
    },
    {
      "package": "wordcloud",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "umap",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "shinydashboard",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "heatmaply",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "utils",
      "role": "Suggests"
    },
    {
      "package": "clusterProfiler",
      "role": "Suggests"
    },
    {
      "package": "DOSE",
      "role": "Suggests"
    },
    {
      "package": "slam",
      "role": "Suggests"
    },
    {
      "package": "org.Ag.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.At.tair.db",
      "role": "Suggests"
    },
    {
      "package": "org.Bt.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Ce.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Cf.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Dm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Dr.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.EcK12.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.EcSakai.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Gg.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mmu.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Pt.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Rn.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Sc.sgd.db",
      "role": "Suggests"
    },
    {
      "package": "org.Ss.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Xl.eg.db",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-30",
      "n": 5
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.24.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "clustering",
    "go",
    "network",
    "pathways",
    "software"
  ],
  "_stars": 36,
  "_contributors": [
    {
      "user": "ssayols",
      "count": 154,
      "uuid": 6011316
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "ssayolsalm",
      "count": 8,
      "uuid": 278362831
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "einarbaldvin",
      "count": 1,
      "uuid": 47445647
    },
    {
      "user": "illumination-k",
      "count": 1,
      "uuid": 43526984
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 944,
    "source": "https://www.bioconductor.org/packages/stats/bioc/rrvgo"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/ssayols/rrvgo",
  "_searchresults": 380,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rrvgo.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ssayols/rrvgo",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateSimMatrix",
    "heatmapPlot",
    "reduceSimMatrix",
    "scatterPlot",
    "shiny_rrvgo",
    "treemapPlot",
    "wordcloudPlot"
  ],
  "_help": [
    {
      "page": "calculateSimMatrix",
      "title": "calculateSimMatrix Calculate the score similarity matrix between terms",
      "topics": [
        "calculateSimMatrix"
      ]
    },
    {
      "page": "getGoSize",
      "title": "getGoSize Get GO term size (# of genes)",
      "topics": [
        "getGoSize"
      ]
    },
    {
      "page": "getGoTerm",
      "title": "getGoTerm Get the description of a GO term",
      "topics": [
        "getGoTerm"
      ]
    },
    {
      "page": "getTermDisp",
      "title": "getTermDisp Calculate the term dispensability score, defined as the semantic similarity threshold a term was assigned to a cluster (namely, the similarity of a term to the cluster representative term).",
      "topics": [
        "getTermDisp"
      ]
    },
    {
      "page": "getTermUniq",
      "title": "getTermUniq Calculate the term uniqueness score, defined as 1 minus the average semantic similarity of a term to all other terms.",
      "topics": [
        "getTermUniq"
      ]
    },
    {
      "page": "gg_color_hue",
      "title": "gg_color_hue Emulate ggplot2 color palette.",
      "topics": [
        "gg_color_hue"
      ]
    },
    {
      "page": "heatmapPlot",
      "title": "heatmapPlot Plot similarity matrix as a heatmap",
      "topics": [
        "heatmapPlot"
      ]
    },
    {
      "page": "loadOrgdb",
      "title": "loadOrgdb Load an orgdb object",
      "topics": [
        "loadOrgdb"
      ]
    },
    {
      "page": "reduceSimMatrix",
      "title": "reduceSimMatrix Reduce a set of GO terms based on their semantic similarity and scores.",
      "topics": [
        "reduceSimMatrix"
      ]
    },
    {
      "page": "scatterPlot",
      "title": "scatterPlot Plot GO terms as scattered points.",
      "topics": [
        "scatterPlot"
      ]
    },
    {
      "page": "shiny_rrvgo",
      "title": "shiny_rrvgo Launch an interactive web interface.",
      "topics": [
        "shiny_rrvgo"
      ]
    },
    {
      "page": "treemapPlot",
      "title": "treemapPlot Plot GO terms as a treemap.",
      "topics": [
        "treemapPlot"
      ]
    },
    {
      "page": "wordcloudPlot",
      "title": "wordlcoudPlot Plot GO reduced terms as a wordcloud.",
      "topics": [
        "wordcloudPlot"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/rrvgo/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "colorspace",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "digest",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "ggrepel",
    "glue",
    "GO.db",
    "GOSemSim",
    "gridBase",
    "gtable",
    "here",
    "htmltools",
    "httpuv",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "NLP",
    "openssl",
    "otel",
    "pheatmap",
    "pkgconfig",
    "png",
    "promises",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "RSpectra",
    "RSQLite",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "slam",
    "sourcetools",
    "sys",
    "tm",
    "treemap",
    "umap",
    "vctrs",
    "viridisLite",
    "withr",
    "wordcloud",
    "xml2",
    "xtable",
    "XVector",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "rrvgo.Rmd",
      "filename": "rrvgo.html",
      "title": "Using the rrvgo package",
      "author": "Sergi Sayols",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to rrvgo",
        "Using rrvgo",
        "Getting started",
        "Calculating the similarity matrix and reducing GO terms",
        "Plotting and interpretation",
        "Similarity matrix heatmap",
        "Scatter plot depicting groups and distance between terms",
        "Treemap plot",
        "Word cloud",
        "Shiny app",
        "Currently supported",
        "Similarity methods",
        "Organisms",
        "Gene Ontologies",
        "Demo data",
        "Citing rrvgo",
        "Reporting problems or bugs",
        "Session info"
      ],
      "created": "2020-02-27 14:07:26",
      "modified": "2023-10-17 12:04:46",
      "commits": 11
    }
  ],
  "_score": 8.789298611159442,
  "_indexed": false,
  "_nocasepkg": "rrvgo",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/rrvgo",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.24.0",
      "date": "2026-05-30T10:52:57.000Z",
      "distro": "noble",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "9d30b922584d29d8b739afe9ef481a3036fcb055fe11ffbd787540e1bd58e13f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.24.0",
      "date": "2026-05-30T10:50:54.000Z",
      "distro": "noble",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "10bccec4e3fdcb2a1cf93423223a2d259ec2b694fd64468d37333635ef76b611",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.24.0",
      "date": "2026-05-30T15:22:25.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "9f83a6e09747647d4d2933e9d151a371dcebac6635b6487cb169166b44844d3e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.24.0",
      "date": "2026-05-30T15:23:04.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "fa3cc2df9f92e5efe48ccfefe47bb0b596b40e2fe28d5db4b555437539f5be83",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.24.0",
      "date": "2026-05-30T10:52:18.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "f5ce7e650ab8ad20b3d1adbaae3cec455fbb0d47c412f72fb76ca7f5ec89a341",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T10:49:36.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "119625bcfa4597d9ebfbbd86f8a5c3686f83703da0b31ecb0e49b3f1ff491874",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T10:50:13.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "ced607faa7395b86d11e3695feac75017569ed35ae6790a1679aaee7dc93d9ef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T10:49:39.000Z",
      "commit": "831eac118ad53b61be846ef704c1c09b9cdd1568",
      "fileid": "8589c1eb36b0274837ce7ef7d131520814103cd3877ebe334c28d75e462ab7df",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680314773"
    }
  ]
}