{
  "_id": "6a493e4da19c9318096e7aa2",
  "Package": "gg4way",
  "Title": "4way Plots of Differential Expression",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(given = c(\"Benjamin\", \"I\"),\nfamily = \"Laufer\",\nrole = c(\"aut\", \"cre\"),\nemail = \"blaufer@gmail.com\"),\nperson(given = c(\"Brad\", \"A\"),\nfamily = \"Friedman\",\nrole = c(\"aut\")))",
  "Description": "4way plots enable a comparison of the logFC values from\ntwo contrasts of differential gene expression. The gg4way\npackage creates 4way plots using the ggplot2 framework and\nsupports popular Bioconductor objects. The package also\nprovides information about the correlation between contrasts\nand significant genes of interest.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/ben-laufer/gg4way",
  "BugReports": "https://github.com/ben-laufer/gg4way/issues",
  "biocViews": "Software, Visualization, DifferentialExpression,\nGeneExpression, Transcription, RNASeq, SingleCell, Sequencing",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "LazyData": "false",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:39 UTC",
  "RemoteUrl": "https://github.com/bioc/gg4way",
  "RemoteRef": "HEAD",
  "RemoteSha": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 03:15:21 UTC",
    "User": "root"
  },
  "Author": "Benjamin I Laufer [aut, cre],\nBrad A Friedman [aut]",
  "Maintainer": "Benjamin I Laufer <blaufer@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "gg4way_1.11.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/3050254d2dbdd9a58258a284eb8f399550ad80db075a473fe5965896b5f26bc2",
  "_filesize": 2882205,
  "_sha256": "3050254d2dbdd9a58258a284eb8f399550ad80db075a473fe5965896b5f26bc2",
  "_expires": "2026-10-12T17:09:31.000Z",
  "_created": "2026-07-04T03:15:21.000Z",
  "_published": "2026-07-04T17:09:33.280Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777",
  "_status": "success",
  "_upstream": "https://github.com/bioc/gg4way",
  "_commit": {
    "id": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
    "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",
    "time": 1777381299
  },
  "_maintainer": {
    "name": "Benjamin I Laufer",
    "email": "blaufer@gmail.com",
    "login": "ben-laufer",
    "linkedin": "in/ben-laufer-539a496a",
    "twitter": "@laufer_ben",
    "description": "Principal Scientist @Genentech",
    "uuid": 43450458
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85150937597,
      "time": 212,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8077826894"
    },
    {
      "job": 85150937616,
      "time": 368,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8077845003"
    },
    {
      "job": 85150937609,
      "time": 373,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8077845610"
    },
    {
      "job": 85150937585,
      "time": 178,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8077822780"
    },
    {
      "job": 85150937636,
      "time": 173,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8077822235"
    },
    {
      "job": 85150937624,
      "time": 312,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8077799836"
    },
    {
      "job": 85150937741,
      "time": 209,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8077826484"
    },
    {
      "job": 85150937641,
      "time": 337,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8077841420"
    },
    {
      "job": 85150937591,
      "time": 506,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8077860755"
    },
    {
      "job": 85150937643,
      "time": 369,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8077845045"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "janitor",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "airway",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "vdiffr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "visualization",
    "differentialexpression",
    "geneexpression",
    "transcription",
    "rnaseq",
    "singlecell",
    "sequencing"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    },
    {
      "user": "ben-laufer",
      "count": 9,
      "uuid": 43450458
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/ben-laufer/gg4way",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gg4way.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ben-laufer/gg4way",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "getCor",
    "getShared",
    "getTotals",
    "gg4way"
  ],
  "_datasets": [
    {
      "name": "airwayFit",
      "title": "airwayFit data",
      "object": "airwayFit",
      "file": "airwayFit.rda",
      "class": [
        "MArrayLM"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "airwayFit",
      "title": "airwayFit data",
      "topics": [
        "airwayFit"
      ]
    },
    {
      "page": "gg4wayExtractors",
      "title": "Helper Functions for 'gg4way'",
      "topics": [
        "extractors",
        "getCor",
        "getShared",
        "getTotals"
      ]
    },
    {
      "page": "gg4way",
      "title": "Create a 4way plot",
      "topics": [
        "gg4way",
        "gg4way.default",
        "gg4way.DESeqDataSet",
        "gg4way.list",
        "gg4way.MArrayLM",
        "gg4way.SimpleList"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/gg4way/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DESeq2",
    "dplyr",
    "edgeR",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "hms",
    "IRanges",
    "isoband",
    "janitor",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "lubridate",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snakecase",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "gg4way.Rmd",
      "filename": "gg4way.html",
      "title": "gg4way",
      "author": "Ben Laufer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Quick start: limma",
        "Prepare data",
        "limma-voom",
        "Plot",
        "Add gene labels",
        "Table for labels",
        "Plotting labels",
        "Advanced options",
        "Axis titles",
        "Correlation only",
        "edgeR",
        "DESeq2",
        "DESeq analysis",
        "Plot by results name",
        "Plot by contrast",
        "Plot by lfcShrink",
        "Other packages",
        "Package support",
        "Session info",
        "References"
      ],
      "created": "2023-08-30 20:10:26",
      "modified": "2024-09-18 19:16:06",
      "commits": 4
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "gg4way",
  "_universes": [
    "bioc",
    "ben-laufer"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-07-04T03:19:24.000Z",
      "distro": "resolute",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/ad13926fd50c2e2af4eb7daf11a45f3fa7c0852f5e4a8431d4eb93a4759492bc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-07-04T03:19:41.000Z",
      "distro": "resolute",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/d845da5e8c56768cd075205d5f8291ab6c7e48bb6b8bb62af0911e0b87cdba6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-07-04T03:17:30.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/20d9d2afac6dd3cdd1e52467e1befc3c52e32c844c4a102d488406865faf23a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-07-04T03:17:27.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/d5bea31bfd079307d22c04f46b080d7481cd96680a39e57de7f6b5ea8c8b821e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-07-04T03:19:23.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/0f2ff1a9d51e0d61d844e4b14726c06d6fec590c88e447f5638f2f8bdbb8692d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-04T03:19:54.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/8f285ccde67e3513559bb9f32e4b3eee07a2592494ebea936fae36c2eb8d53a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-04T03:21:50.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/345d0c26530c8848ec1e8b8c35128aa61862903288a6462718dccdd99f2678ee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-04T03:20:23.000Z",
      "commit": "6d25c07768b137d4e2a623e0dc4a07c15a50234e",
      "fileid": "https://r2.ropensci.org/fbc58a4829b077158690b12816db0258b06047722b95be5c023816d10f126915",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693116777"
    }
  ]
}