{
  "_id": "6a34f66c3efcd9bda43d339e",
  "Package": "famat",
  "Title": "Functional analysis of metabolic and transcriptomic data",
  "Version": "1.22.0",
  "Description": "Famat is made to collect data about lists of genes and\nmetabolites provided by user, and to visualize it through a\nShiny app. Information collected is: - Pathways containing some\nof the user's genes and metabolites (obtained using a pathway\nenrichment analysis). - Direct interactions between user's\nelements inside pathways. - Information about elements (their\nidentifiers and descriptions). - Go terms enrichment analysis\nperformed on user's genes. The Shiny app is composed of: -\ninformation about genes, metabolites, and direct interactions\nbetween them inside pathways. - an heatmap showing which\nelements from the list are in pathways (pathways are structured\nin hierarchies). - hierarchies of enriched go terms using\nMolecular Function and Biological Process.",
  "Authors@R": "person(given = \"Mathieu\",\nfamily = \"Charles\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mathieu.charles@inrae.fr\",\ncomment = c(ORCID = \"0000-0001-5343-6324\"))",
  "License": "GPL-3",
  "LazyData": "false",
  "VignetteBuilder": "knitr",
  "biocViews": "FunctionalPrediction, GeneSetEnrichment, Pathways, GO,\nReactome, KEGG",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.1",
  "BugReports": "https://github.com/emiliesecherre/famat/issues",
  "URL": "https://github.com/emiliesecherre/famat",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:16 UTC",
  "RemoteUrl": "https://github.com/bioc/famat",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-19 07:42:33 UTC",
    "User": "root"
  },
  "Author": "Mathieu Charles [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5343-6324>)",
  "Maintainer": "Mathieu Charles <mathieu.charles@inrae.fr>",
  "MD5sum": "c52c2ac5de88416a6bd7d61326af784e",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "famat_1.22.0.tar.gz",
  "_fileid": "4e08c831f8ff14c9ca4c18724dc58a16f3623ec65aae8ae95cf7ee2ebf00def2",
  "_filesize": 4134383,
  "_sha256": "4e08c831f8ff14c9ca4c18724dc58a16f3623ec65aae8ae95cf7ee2ebf00def2",
  "_created": "2026-06-19T07:42:33.000Z",
  "_published": "2026-06-19T07:57:32.499Z",
  "_jobs": [
    {
      "job": 82306148707,
      "time": 283,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7744381637"
    },
    {
      "job": 82306148700,
      "time": 701,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7744505091"
    },
    {
      "job": 82306148810,
      "time": 700,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7744504688"
    },
    {
      "job": 82306148678,
      "time": 431,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7744520016"
    },
    {
      "job": 82306148712,
      "time": 520,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7744547983"
    },
    {
      "job": 82305135080,
      "time": 446,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7744300297"
    },
    {
      "job": 82306148675,
      "time": 254,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7744373202"
    },
    {
      "job": 82306148731,
      "time": 678,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7744498133"
    },
    {
      "job": 82306148716,
      "time": 581,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7744469661"
    },
    {
      "job": 82306148784,
      "time": 659,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7744492766"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/famat",
  "_commit": {
    "id": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
    "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": 1777380856
  },
  "_maintainer": {
    "name": "Mathieu Charles",
    "email": "mathieu.charles@inrae.fr",
    "login": "mathieucharlesinrae",
    "description": "",
    "uuid": 74656392,
    "orcid": "0000-0001-5343-6324"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "KEGGREST",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiasedUrn",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "gprofiler2",
      "role": "Imports"
    },
    {
      "package": "rWikiPathways",
      "role": "Imports"
    },
    {
      "package": "reactome.db",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "ontologyIndex",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinydashboard",
      "role": "Imports"
    },
    {
      "package": "shinyBS",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "ReactomePA",
      "role": "Imports"
    },
    {
      "package": "enrichplot",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-03",
      "n": 1
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "functionalprediction",
    "genesetenrichment",
    "pathways",
    "go",
    "reactome",
    "kegg",
    "compound",
    "gene-ontology",
    "genes",
    "shiny"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "emiliesecherre",
      "count": 43,
      "uuid": 56070732
    },
    {
      "user": "mathieucharlesinrae",
      "count": 31,
      "uuid": 74656392
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/emiliesecherre/famat",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/famat.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/emiliesecherre/famat",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "compl_data",
    "interactions",
    "path_enrich",
    "rshiny"
  ],
  "_datasets": [
    {
      "name": "all_compounds_chebi",
      "title": "",
      "object": "all_compounds_chebi",
      "file": "all_compounds_chebi.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chebi_id",
        "pathway_kegg",
        "pathway_reactome",
        "pathway_wiki",
        "chebi_name",
        "kegg_id",
        "kegg_name"
      ],
      "rows": 5467,
      "table": true,
      "tojson": true
    },
    {
      "name": "compl_data_result",
      "title": "Output of 'compl_data' function",
      "object": "compl_data_result",
      "file": "compl_data_result.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "genes",
      "title": "List of genes.",
      "object": "genes",
      "file": "genes.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "interactions_result",
      "title": "Output of 'interactions' function",
      "object": "interactions_result",
      "file": "interactions_result.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "listk",
      "title": "Pathway enrichment analysis results for KEGG pathways.",
      "object": "listk",
      "file": "listk.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "listr",
      "title": "Pathway enrichment analysis results for Reactome pathways.",
      "object": "listr",
      "file": "listr.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "listw",
      "title": "Pathway enrichment analysis results for Wikipathways pathways.",
      "object": "listw",
      "file": "listw.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "meta",
      "title": "List of metabolites.",
      "object": "meta",
      "file": "meta.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MPINetData",
      "title": "The variables in the environment variable 'MPINetData' of the system",
      "object": "MPINetData",
      "file": "MPINetData.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "compl_data",
      "title": "Data preparation for Shiny interface",
      "topics": [
        "compl_data"
      ]
    },
    {
      "page": "compl_data_result",
      "title": "Output of 'compl_data' function",
      "topics": [
        "compl_data_result"
      ]
    },
    {
      "page": "genes",
      "title": "List of genes.",
      "topics": [
        "genes"
      ]
    },
    {
      "page": "interactions",
      "title": "Interactions between genes and metabolites",
      "topics": [
        "interactions"
      ]
    },
    {
      "page": "interactions_result",
      "title": "Output of 'interactions' function",
      "topics": [
        "interactions_result"
      ]
    },
    {
      "page": "listk",
      "title": "Pathway enrichment analysis results for KEGG pathways.",
      "topics": [
        "listk"
      ]
    },
    {
      "page": "listr",
      "title": "Pathway enrichment analysis results for Reactome pathways.",
      "topics": [
        "listr"
      ]
    },
    {
      "page": "listw",
      "title": "Pathway enrichment analysis results for Wikipathways pathways.",
      "topics": [
        "listw"
      ]
    },
    {
      "page": "meta",
      "title": "List of metabolites.",
      "topics": [
        "meta"
      ]
    },
    {
      "page": "MPINetData",
      "title": "The variables in the environment variable 'MPINetData' of the system",
      "topics": [
        "consensusPath",
        "getBackground",
        "getnodeseq",
        "getpathList('KEGG')",
        "getStr",
        "MPINetData"
      ]
    },
    {
      "page": "path_enrich",
      "title": "Pathway enrichment analysis",
      "topics": [
        "path_enrich"
      ]
    },
    {
      "page": "rshiny",
      "title": "Shiny interface",
      "topics": [
        "rshiny"
      ]
    }
  ],
  "_rundeps": [
    "aisdk",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "base64enc",
    "BiasedUrn",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "callr",
    "cli",
    "clipr",
    "cluster",
    "clusterProfiler",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "digest",
    "dir.expiry",
    "DOSE",
    "dplyr",
    "DT",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "fs",
    "gdtools",
    "generics",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggraph",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "gprofiler2",
    "graph",
    "graphite",
    "graphlayouts",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mgcv",
    "mime",
    "nlme",
    "ontologyIndex",
    "openssl",
    "org.Hs.eg.db",
    "otel",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "prettyunits",
    "processx",
    "progress",
    "promises",
    "ps",
    "purrr",
    "qvalue",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "reactome.db",
    "ReactomePA",
    "readr",
    "reshape2",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "rWikiPathways",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "Seqinfo",
    "shiny",
    "shinyBS",
    "shinydashboard",
    "sourcetools",
    "stringi",
    "stringr",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timechange",
    "tinytex",
    "treeio",
    "tweenr",
    "tzdb",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "famat.Rmd",
      "filename": "famat.html",
      "title": "famat",
      "author": "Emilie Secherre",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "path_enrich",
        "interactions",
        "compl_data",
        "rshiny",
        "Conclusion: how to use famat",
        "References",
        "Session Info"
      ],
      "created": "2020-09-29 14:53:55",
      "modified": "2026-01-26 15:14:05",
      "commits": 5
    }
  ],
  "_score": 4.2552725051033065,
  "_indexed": false,
  "_nocasepkg": "famat",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/famat",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.22.0",
      "date": "2026-06-19T07:47:37.000Z",
      "distro": "noble",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "d809e4df9f2be21017f8a863f4718b282561ce45c5a59339081621374f0a0e44",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.22.0",
      "date": "2026-06-19T07:47:37.000Z",
      "distro": "noble",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "1d88e4b381cbd98a4263f61d16bfd580e0fb653da1c0ddeb5bf1e094de40add9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.22.0",
      "date": "2026-06-19T07:50:22.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "4f77d5a03fa4ddcc11ebc19376905c17e720d3f023d1488b1cb0e81d89702f27",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.22.0",
      "date": "2026-06-19T07:50:28.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "8a441c9db4e00a77a863392631c30db318556a6e65ec2d3981b89031e06ef2e0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.22.0",
      "date": "2026-06-19T07:47:13.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "233f5c47117474f79adfba8c5cc78c29c811cba933cf48dffe601dfb9040709d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-06-19T07:45:41.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "e4f72856e70d748a542e1472807536b67241c0283ca4c4695b9aed364e412f70",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-06-19T07:45:18.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "3c078a09dfc14e20941f993d0281b3d619f14adb6b5ab2260d1c5b88e02caba0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-06-19T07:45:29.000Z",
      "commit": "df289f03a0a89f3d8d872a0ebe24519d1fc508a4",
      "fileid": "c56661d260f38b60b420d74cf70ff1c432be18953a9c6e9529f14b2aa270127d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812257510"
    }
  ]
}