{
  "_id": "6a328bac3efcd9bda438cb59",
  "Package": "GraphExperiment",
  "Title": "S4 Class for Quantitative Data and Associated Networks",
  "Version": "1.1.2",
  "Date": "2026-03-01",
  "Authors@R": "c(\nperson(given = \"Fabricio\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\"))\n)",
  "Description": "GraphExperiment provides users and developers with an S4\nclass that extends `SingleCellExperiment` by offering\ninfrastructure to store and retrieve networks (`igraph`\nobjects) representing how assay features and/or observations\nare associated with each other. The class was designed to store\nnetworks inferred from high-dimensional quantitative data, with\nfeature-feature networks including gene coexpression networks\n(GCNs), gene regulatory networks (GRNs), and co-abundance\nnetworks (from proteomics and metabolomics), and\nobservation-observation network including cell-cell distances,\nspecies-species relationships, and sample-sample similarities.",
  "License": "GPL-3",
  "URL": "https://github.com/almeidasilvaf/GraphExperiment",
  "BugReports": "https://support.bioconductor.org/tag/GraphExperiment",
  "Encoding": "UTF-8",
  "biocViews": "DataRepresentation, DataImport, Infrastructure,\nGeneExpression, Transcriptomics, Network, SingleCell",
  "Config/testthat/edition": "3",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-17 07:50:08 UTC",
  "RemoteUrl": "https://github.com/bioc/GraphExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-17 11:50:59 UTC",
    "User": "root"
  },
  "Author": "Fabricio Almeida-Silva [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5314-2964>)",
  "Maintainer": "Fabricio Almeida-Silva <fabricio_almeidasilva@hotmail.com>",
  "MD5sum": "15abfe37d7f5b85a6adaac77c541e7ad",
  "_user": "bioc",
  "_type": "src",
  "_file": "GraphExperiment_1.1.2.tar.gz",
  "_fileid": "4778819d66ccac56a6f17b737583206f0666823e11e319c6241ae3434759bdc9",
  "_filesize": 1128298,
  "_sha256": "4778819d66ccac56a6f17b737583206f0666823e11e319c6241ae3434759bdc9",
  "_created": "2026-06-17T11:50:59.000Z",
  "_published": "2026-06-17T11:57:32.616Z",
  "_jobs": [
    {
      "job": 81887860507,
      "time": 291,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7694599210"
    },
    {
      "job": 81887860505,
      "time": 272,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7694594279"
    },
    {
      "job": 81887860480,
      "time": 264,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7694592043"
    },
    {
      "job": 81887860547,
      "time": 173,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7694559195"
    },
    {
      "job": 81887860482,
      "time": 138,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7694545855"
    },
    {
      "job": 81886927642,
      "time": 313,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7694491044"
    },
    {
      "job": 81887860510,
      "time": 126,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7694539709"
    },
    {
      "job": 81887860486,
      "time": 208,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7694568896"
    },
    {
      "job": 81887860506,
      "time": 186,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7694559690"
    },
    {
      "job": 81887860536,
      "time": 167,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7694553122"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GraphExperiment",
  "_commit": {
    "id": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
    "author": "almeidasilvaf <fabricio_almeidasilva@hotmail.com>",
    "committer": "almeidasilvaf <fabricio_almeidasilva@hotmail.com>",
    "message": "Version bump in devel\n",
    "time": 1781682608
  },
  "_maintainer": {
    "name": "Fabricio Almeida-Silva",
    "email": "fabricio_almeidasilva@hotmail.com",
    "login": "almeidasilvaf",
    "bluesky": "@almeidasilvaf.bsky.social",
    "description": "Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.",
    "uuid": 61153286,
    "orcid": "0000-0002-5314-2964"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocBaseUtils",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 13
    },
    {
      "week": "2026-11",
      "n": 3
    },
    {
      "week": "2026-12",
      "n": 13
    },
    {
      "week": "2026-15",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 2
    },
    {
      "week": "2026-25",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "datarepresentation",
    "dataimport",
    "infrastructure",
    "geneexpression",
    "transcriptomics",
    "network",
    "singlecell",
    "bioconductor",
    "bioinformatics",
    "oop"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "almeidasilvaf",
      "count": 37,
      "uuid": 61153286
    },
    {
      "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/almeidasilvaf/graphexperiment",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GraphExperiment.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/almeidasilvaf/graphexperiment",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "colData",
    "colGraph",
    "colGraph<-",
    "colGraphNames",
    "colGraphNames<-",
    "colGraphs",
    "colGraphs<-",
    "GraphExperiment",
    "rowData",
    "rowGraph",
    "rowGraph<-",
    "rowGraphNames",
    "rowGraphNames<-",
    "rowGraphs",
    "rowGraphs<-"
  ],
  "_help": [
    {
      "page": "GraphExperiment",
      "title": "'GraphExperiment' S4 class",
      "topics": [
        "GraphExperiment",
        "GraphExperiment-class"
      ]
    },
    {
      "page": "GraphExperiment-coerce",
      "title": "Coercion methods for 'GraphExperiment' objects",
      "topics": [
        "coerce,RangedSummarizedExperiment,GraphExperiment-method",
        "coerce,SingleCellExperiment,GraphExperiment-method",
        "coerce,SummarizedExperiment,GraphExperiment-method",
        "GraphExperiment-coerce"
      ]
    },
    {
      "page": "GraphExperiment-methods",
      "title": "Methods for 'GraphExperiment' objects",
      "topics": [
        "colData",
        "colData,GraphExperiment-method",
        "colGraph",
        "colGraph,GraphExperiment,ANY-method",
        "colGraph,GraphExperiment,missing-method",
        "colGraph<-",
        "colGraph<-,GraphExperiment-method",
        "colGraphNames",
        "colGraphNames,GraphExperiment-method",
        "colGraphNames<-",
        "colGraphNames<-,GraphExperiment,character-method",
        "colGraphs",
        "colGraphs,GraphExperiment-method",
        "colGraphs<-",
        "colGraphs<-,GraphExperiment-method",
        "GraphExperiment-methods",
        "rowData",
        "rowData,GraphExperiment-method",
        "rowGraph",
        "rowGraph,GraphExperiment,ANY-method",
        "rowGraph,GraphExperiment,missing-method",
        "rowGraph<-",
        "rowGraph<-,GraphExperiment-method",
        "rowGraphNames",
        "rowGraphNames,GraphExperiment-method",
        "rowGraphNames<-",
        "rowGraphNames<-,GraphExperiment,character-method",
        "rowGraphs",
        "rowGraphs,GraphExperiment-method",
        "rowGraphs<-",
        "rowGraphs<-,GraphExperiment-method"
      ]
    },
    {
      "page": "GraphExperiment-subset",
      "title": "Subsetting 'GraphExperiment' objects",
      "topics": [
        "GraphExperiment-subset",
        "[,GraphExperiment,ANY,ANY,ANY-method"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/GraphExperiment/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/GraphExperiment/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "generics",
    "GenomicRanges",
    "glue",
    "igraph",
    "IRanges",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pkgconfig",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "SparseArray",
    "SummarizedExperiment",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "GraphExperiment.Rmd",
      "filename": "GraphExperiment.html",
      "title": "Introduction to the GraphExperiment class",
      "author": "Fabricio Almeida-Silva",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Anatomy of a GraphExperiment object",
        "Building a GraphExperiment object",
        "Accessing rowGraphs/colGraphs and rowData/colData (a.k.a. 'getters')",
        "Modifying GraphExperiment objects (a.k.a. 'setters')",
        "Subsetting GraphExperiment objects",
        "Session information",
        "References"
      ],
      "created": "2026-03-16 09:51:01",
      "modified": "2026-06-17 07:49:50",
      "commits": 5
    }
  ],
  "_score": 4.544068044350276,
  "_indexed": true,
  "_nocasepkg": "graphexperiment",
  "_universes": [
    "bioc",
    "almeidasilvaf"
  ],
  "_previous": "1.1.1",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.2",
      "date": "2026-06-17T11:54:52.000Z",
      "distro": "noble",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "6750aee25591b8dd6d81d2b35e8c03ed6c9daebeb04f937dba156567e88fbf7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.2",
      "date": "2026-06-17T11:54:52.000Z",
      "distro": "noble",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "b75990e19916638ac806c8b5ea081a10c52a2955c3a7f541ad62678c69e47b0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.2",
      "date": "2026-06-17T11:53:54.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "78d4ecc16c276e8253e5759111f41ba68c9cebed31828c2e6cb0ec62ca29cfe7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.2",
      "date": "2026-06-17T11:53:41.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "77468c7417c54e293ddd1f9411355923b4a1ce571ae26987938fbe5bf53adc79",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.2",
      "date": "2026-06-17T11:54:33.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "d2fc26962e2b98c5538b2a1df44955718496da364d25bbe1c512e2ac815ca239",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.2",
      "date": "2026-06-17T11:53:31.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "1d78ba514365a18c59ae8733f163fd4421e0a70e727a45bc4ec35507e9a28c46",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.2",
      "date": "2026-06-17T11:53:29.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "1104647cbc882822fa362bbbb156407c45a4041f5e38bb877854b2bad7a6b2f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.2",
      "date": "2026-06-17T11:53:32.000Z",
      "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef",
      "fileid": "597acb9de37bd0d293a75ff77642194b44a872613753b5b605d2ae3074455543",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27686643074"
    }
  ]
}