{
  "_id": "6a101abbacfb0bcc41c86a99",
  "Package": "gatom",
  "Title": "Finding an Active Metabolic Module in Atom Transition Network",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(\"Anastasiia\", \"Gainullina\", role = c(\"aut\")),\nperson(\"Mariia\", \"Emelianova\", role = c(\"aut\")),\nperson(\"Alexey\", \"Sergushichev\", email = \"alsergbox@gmail.com\", role = c(\"aut\", \"cre\")))",
  "Description": "This package implements a metabolic network analysis\npipeline to identify an active metabolic module based on high\nthroughput data. The pipeline takes as input transcriptional\nand/or metabolic data and finds a metabolic subnetwork (module)\nmost regulated between the two conditions of interest. The\npackage further provides functions for module post-processing,\nannotation and visualization.",
  "biocViews": "GeneExpression, DifferentialExpression, Pathways, Network",
  "License": "MIT + file LICENCE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/ctlab/gatom/",
  "BugReports": "https://github.com/ctlab/gatom/issues",
  "Config/pak/sysreqs": "cmake libglpk-dev make default-jdk libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:45 UTC",
  "RemoteUrl": "https://github.com/bioc/gatom",
  "RemoteRef": "HEAD",
  "RemoteSha": "736ab92b6cb72cc085c4269a293d006063ff23cc",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-14 09:48:33 UTC",
    "User": "root"
  },
  "Author": "Anastasiia Gainullina [aut],\nMariia Emelianova [aut],\nAlexey Sergushichev [aut, cre]",
  "Maintainer": "Alexey Sergushichev <alsergbox@gmail.com>",
  "MD5sum": "f168bb9ecee86e3e9168bd20296460e1",
  "_user": "bioc",
  "_type": "src",
  "_file": "gatom_1.11.0.tar.gz",
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  "_created": "2026-05-14T09:48:33.000Z",
  "_published": "2026-05-22T08:58:35.933Z",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25853118303",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/gatom",
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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": "Alexey Sergushichev",
    "email": "alsergbox@gmail.com",
    "login": "assaron",
    "bluesky": "@asergushichev.bsky.social",
    "twitter": "@assaron",
    "uuid": 1040217
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      "version": ">= 4.3.0",
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      "package": "data.table",
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    },
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      "package": "igraph",
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    },
    {
      "package": "BioNet",
      "role": "Imports"
    },
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      "package": "plyr",
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    },
    {
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    },
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    },
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    },
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      "package": "intergraph",
      "role": "Imports"
    },
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    },
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      "package": "ggnetwork",
      "role": "Imports"
    },
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    },
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      "package": "grid",
      "role": "Imports"
    },
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    },
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      "package": "mwcsr",
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    },
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      "role": "Suggests"
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    },
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      "package": "KEGGREST",
      "role": "Suggests"
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      "package": "AnnotationDbi",
      "role": "Suggests"
    },
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      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "reactome.db",
      "role": "Suggests"
    },
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      "package": "fgsea",
      "role": "Suggests"
    },
    {
      "package": "readr",
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    },
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      "package": "BiocStyle",
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 2
    },
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      "n": 3
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  "_bioc": [
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      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
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      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression",
    "differentialexpression",
    "pathways",
    "network"
  ],
  "_stars": 8,
  "_contributors": [
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      "user": "assaron",
      "count": 120,
      "uuid": 1040217
    },
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 312,
    "source": "https://www.bioconductor.org/packages/stats/bioc/gatom"
  },
  "_devurl": "https://github.com/ctlab/gatom",
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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    "extra/gatom.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ctlab/gatom",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "abbreviateLabels",
    "addHighlyExpressedEdges",
    "collapseAtomsIntoMetabolites",
    "connectAtomsInsideMetabolite",
    "createShinyCyJSWidget",
    "getGeneDEMeta",
    "getMetDEMeta",
    "makeMetabolicGraph",
    "makeOrgGatomAnnotation",
    "prepareDE",
    "saveModuleToDot",
    "saveModuleToHtml",
    "saveModuleToPdf",
    "saveModuleToXgmml",
    "scoreGraph"
  ],
  "_datasets": [
    {
      "name": "gene.de.rawEx",
      "title": "Example gene differential expression data.",
      "object": "gene.de.rawEx",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ID",
        "pval",
        "log2FC",
        "baseMean"
      ],
      "rows": 617,
      "table": true,
      "tojson": true
    },
    {
      "name": "gEx",
      "title": "Example metabolic graph with atom topology.",
      "object": "gEx",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gsEx",
      "title": "Example scored metabolic graph with atom topology.",
      "object": "gsEx",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "met.de.rawEx",
      "title": "Example metabolite differential abundance data.",
      "object": "met.de.rawEx",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ID",
        "pval",
        "log2FC",
        "baseMean"
      ],
      "rows": 54,
      "table": true,
      "tojson": true
    },
    {
      "name": "met.kegg.dbEx",
      "title": "Example KEGG-based metabolite database object",
      "object": "met.kegg.dbEx",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mEx",
      "title": "Example metabolic module.",
      "object": "mEx",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "networkEx",
      "title": "Example KEGG-based network object",
      "object": "networkEx",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "org.Mm.eg.gatom.annoEx",
      "title": "Example organism annotation object",
      "object": "org.Mm.eg.gatom.annoEx",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "abbreviateLabels",
      "title": "Abbreviate lipid labels for lipid module",
      "topics": [
        "abbreviateLabels"
      ]
    },
    {
      "page": "addHighlyExpressedEdges",
      "title": "Add reactions without highly changing genes but with high average expression",
      "topics": [
        "addHighlyExpressedEdges"
      ]
    },
    {
      "page": "collapseAtomsIntoMetabolites",
      "title": "Collapse atoms belonging to the same metabolite into one vertex",
      "topics": [
        "collapseAtomsIntoMetabolites"
      ]
    },
    {
      "page": "connectAtomsInsideMetabolite",
      "title": "Connect atoms belonging to the same metabolite with edges",
      "topics": [
        "connectAtomsInsideMetabolite"
      ]
    },
    {
      "page": "createShinyCyJSWidget",
      "title": "Creates shinyCyJS widget from module",
      "topics": [
        "createShinyCyJSWidget"
      ]
    },
    {
      "page": "gene.de.rawEx",
      "title": "Example gene differential expression data.",
      "topics": [
        "gene.de.rawEx"
      ]
    },
    {
      "page": "getGeneDEMeta",
      "title": "Finds columns in gene differential expression table required for gatom analysis",
      "topics": [
        "getGeneDEMeta"
      ]
    },
    {
      "page": "getMetabolicPathways",
      "title": "Generate list of metabolic pathways from Reactome and KEGG databases",
      "topics": [
        "getMetabolicPathways"
      ]
    },
    {
      "page": "getMetDEMeta",
      "title": "Finds columns in differential expression table for metabolites required for gatom analysis",
      "topics": [
        "getMetDEMeta"
      ]
    },
    {
      "page": "gEx",
      "title": "Example metabolic graph with atom topology.",
      "topics": [
        "gEx"
      ]
    },
    {
      "page": "gsEx",
      "title": "Example scored metabolic graph with atom topology.",
      "topics": [
        "gsEx"
      ]
    },
    {
      "page": "makeMetabolicGraph",
      "title": "Creates metabolic graph based on specified data",
      "topics": [
        "makeMetabolicGraph"
      ]
    },
    {
      "page": "makeOrgGatomAnnotation",
      "title": "Create an organism annotation object for network analysis",
      "topics": [
        "makeOrgGatomAnnotation"
      ]
    },
    {
      "page": "met.de.rawEx",
      "title": "Example metabolite differential abundance data.",
      "topics": [
        "met.de.rawEx"
      ]
    },
    {
      "page": "met.kegg.dbEx",
      "title": "Example KEGG-based metabolite database object",
      "topics": [
        "met.kegg.dbEx"
      ]
    },
    {
      "page": "mEx",
      "title": "Example metabolic module.",
      "topics": [
        "mEx"
      ]
    },
    {
      "page": "networkEx",
      "title": "Example KEGG-based network object",
      "topics": [
        "networkEx"
      ]
    },
    {
      "page": "org.Mm.eg.gatom.annoEx",
      "title": "Example organism annotation object",
      "topics": [
        "org.Mm.eg.gatom.annoEx"
      ]
    },
    {
      "page": "prepareDE",
      "title": "Makes data.table with differential expression results containing all columns required for gatom and in the expected format based on metadata object",
      "topics": [
        "prepareDE"
      ]
    },
    {
      "page": "saveModuleToDot",
      "title": "Save module to a graphviz dot file",
      "topics": [
        "saveModuleToDot"
      ]
    },
    {
      "page": "saveModuleToHtml",
      "title": "Save module to a html widget",
      "topics": [
        "saveModuleToHtml"
      ]
    },
    {
      "page": "saveModuleToPdf",
      "title": "Save module to a nice pdf file",
      "topics": [
        "saveModuleToPdf"
      ]
    },
    {
      "page": "saveModuleToXgmml",
      "title": "Save module to an XGMML file",
      "topics": [
        "saveModuleToXgmml"
      ]
    },
    {
      "page": "scoreGraph",
      "title": "Score metabolic graph",
      "topics": [
        "scoreGraph"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/gatom/raw/HEAD/README.md",
  "_rundeps": [
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    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shinyCyJS",
    "sna",
    "statnet.common",
    "sys",
    "tibble",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
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    "yaml"
  ],
  "_vignettes": [
    {
      "source": "gatom-tutorial.Rmd",
      "filename": "gatom-tutorial.html",
      "title": "Using gatom package",
      "author": "Anstasiia Gainullina, Mariia Emelianova, Alexey Sergushichev",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Example workfow",
        "Saving modules",
        "Example on full data and full network",
        "Networks",
        "KEGG",
        "Rhea",
        "Combined network",
        "Rhea lipid subnetwork",
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        "Running with no metabolite data",
        "Running with no gene data",
        "Using metabolite-level network",
        "Pathway annotation"
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      "created": "2018-03-09 12:45:14",
      "modified": "2023-10-15 03:13:19",
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  "_indexed": true,
  "_nocasepkg": "gatom",
  "_universes": [
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