{ "_id": "6a59f0d409eb0996dd68fb35", "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": "2026-07-17 09:00:38 UTC", "User": "root" }, "Author": "Fabricio Almeida-Silva [aut, cre] (ORCID:\n)", "Maintainer": "Fabricio Almeida-Silva ", "_user": "bioc", "_type": "src", "_file": "GraphExperiment_1.1.2.tar.gz", "_fileid": "https://r2.ropensci.org/e57487387ed8ef157dbaaa5a8b6ebca49c0a670dcbc5d013842181a62d12b444", "_filesize": 1127202, "_sha256": "e57487387ed8ef157dbaaa5a8b6ebca49c0a670dcbc5d013842181a62d12b444", "_expires": "2026-10-25T09:07:29.000Z", "_created": "2026-07-17T09:00:38.000Z", "_published": "2026-07-17T09:07:32.183Z", "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088", "_status": "success", "_upstream": "https://github.com/bioc/GraphExperiment", "_commit": { "id": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "author": "almeidasilvaf ", "committer": "almeidasilvaf ", "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": "resolute", "_jobs": [ { "job": 87846428560, "time": 178, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8402137087" }, { "job": 87846428823, "time": 273, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8402175086" }, { "job": 87846428612, "time": 339, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8402200409" }, { "job": 87846428626, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8402127254" }, { "job": 87846428627, "time": 146, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8402124261" }, { "job": 87845597129, "time": 264, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8402065079" }, { "job": 87846428594, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8402123095" }, { "job": 87846428623, "time": 281, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8402185575" }, { "job": 87846428628, "time": 221, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8402154219" }, { "job": 87846428599, "time": 194, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8402143014" } ], "_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": "1.1.2", "bioc": "3.24" }, { "branch": "release", "version": "1.0.2", "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": 447, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 256, "source": "https://www.bioconductor.org/packages/stats/bioc/GraphExperiment" }, "_devurl": "https://github.com/almeidasilvaf/graphexperiment", "_searchresults": 2, "_rbuild": "4.6.1", "_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" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-07-17T09:03:48.000Z", "distro": "resolute", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/196d08091e31e4424445b203c424f690d12af6dcefac83aad3cca61c695b2e1f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.6.1", "os": "linux", "version": "1.1.2", "date": "2026-07-17T09:04:49.000Z", "distro": "resolute", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/c505bc0a86bc60398ab51b08b96c035f688ce7040f4e246d9433d09ca54c7320", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.5.3", "os": "mac", "version": "1.1.2", "date": "2026-07-17T09:02:29.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/c08f73d77cd9bd4cd634e2e8fdf702f16bb09e3850141cd348cc52a24fedd28f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.6.1", "os": "mac", "version": "1.1.2", "date": "2026-07-17T09:02:34.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/7eed1c38c30d86f7ee0743e17e71a241dd309bf96ddfaf43a2e3001ee87a0207", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.2", "date": "2026-07-17T09:03:41.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/32acddc0770e6ad0f0f155d2f2b2fa1832168514b6c8893911f3c407f77b7853", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.7.0", "os": "win", "version": "1.1.2", "date": "2026-07-17T09:03:46.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/5fb729fb56494213fc6961373df04de005bba1869aa6916f93275509f5a39a5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.5.3", "os": "win", "version": "1.1.2", "date": "2026-07-17T09:03:10.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/b78cb177658cc4d661fab4228857afa5bcc35f19f0e932e43aaa04ab51da314c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" }, { "r": "4.6.1", "os": "win", "version": "1.1.2", "date": "2026-07-17T09:02:22.000Z", "commit": "a7e32171d97d7c99cf0968c577884a333d11f9ef", "fileid": "https://r2.ropensci.org/ea2abdaf05da268583ef774f1c51187bd34e1d79297ee69da0663c0cb417aacc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29568190088" } ] }