{
  "_id": "6a49437f18cdde069385ebfe",
  "Package": "edge",
  "Type": "Package",
  "Title": "Extraction of Differential Gene Expression",
  "Date": "2015-04-15",
  "Version": "2.45.0",
  "Author": "John D. Storey, Jeffrey T. Leek and Andrew J. Bass",
  "Maintainer": "John D. Storey <jstorey@princeton.edu>, Andrew J. Bass\n<ajbass@emory.edu>",
  "biocViews": "MultipleComparison, DifferentialExpression, TimeCourse,\nRegression, GeneExpression, DataImport",
  "Description": "The edge package implements methods for carrying out\ndifferential expression analyses of genome-wide gene expression\nstudies. Significance testing using the optimal discovery\nprocedure and generalized likelihood ratio tests (equivalent to\nF-tests and t-tests) are implemented for general study designs.\nSpecial functions are available to facilitate the analysis of\ncommon study designs, including time course experiments. Other\npackages such as sva and qvalue are integrated in edge to\nprovide a wide range of tools for gene expression analysis.",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/jdstorey/edge",
  "BugReports": "https://github.com/jdstorey/edge/issues",
  "LazyData": "true",
  "License": "MIT + file LICENSE",
  "NeedsCompilation": "yes",
  "RoxygenNote": "5.0.1",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:17 UTC",
  "RemoteUrl": "https://github.com/bioc/edge",
  "RemoteRef": "HEAD",
  "RemoteSha": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
  "Packaged": {
    "Date": "2026-07-04 12:56:36 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "edge_2.45.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d88927dc9bf9310a6739f0212e2e30428de17cb074bbf9097a965a0525bfdc57",
  "_filesize": 1193757,
  "_sha256": "d88927dc9bf9310a6739f0212e2e30428de17cb074bbf9097a965a0525bfdc57",
  "_expires": "2026-10-12T17:31:41.000Z",
  "_created": "2026-07-04T12:56:36.000Z",
  "_published": "2026-07-04T17:31:43.542Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107",
  "_status": "success",
  "_upstream": "https://github.com/bioc/edge",
  "_commit": {
    "id": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
    "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": 1777380077
  },
  "_maintainer": {
    "name": "John D. Storey",
    "email": "ajbass@emory.edu",
    "login": "jdstorey",
    "description": "I'm a professor at Princeton University working in statistics, genomics & data science.  See my lab's GitHub, @StoreyLab, for our software development. ",
    "uuid": 6211610
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85152466235,
      "time": 173,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8081920500"
    },
    {
      "job": 85152466026,
      "time": 245,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8081929757"
    },
    {
      "job": 85152466213,
      "time": 293,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8081935144"
    },
    {
      "job": 85152466112,
      "time": 270,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8081932966"
    },
    {
      "job": 85152466277,
      "time": 284,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8081934089"
    },
    {
      "job": 85152466143,
      "time": 137,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8081916357"
    },
    {
      "job": 85152466084,
      "time": 304,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8081936406"
    },
    {
      "job": 85152466074,
      "time": 171,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8081919984"
    },
    {
      "job": 85152466090,
      "time": 290,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8081934645"
    },
    {
      "job": 85152465911,
      "time": 271,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081900575"
    },
    {
      "job": 85152466057,
      "time": 169,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8081919870"
    },
    {
      "job": 85152466142,
      "time": 252,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8081930149"
    },
    {
      "job": 85152466152,
      "time": 216,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8081925754"
    },
    {
      "job": 85152466180,
      "time": 220,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8081926340"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "version": ">= 1.99.0",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "reshape2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.45.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.44.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "multiplecomparison",
    "differentialexpression",
    "timecourse",
    "regression",
    "geneexpression",
    "dataimport"
  ],
  "_stars": 21,
  "_contributors": [
    {
      "user": "ajbass",
      "count": 119,
      "uuid": 7573657
    },
    {
      "user": "jdstorey",
      "count": 15,
      "uuid": 6211610
    },
    {
      "user": "ncchung",
      "count": 7,
      "uuid": 8022966
    },
    {
      "user": "slowkow",
      "count": 1,
      "uuid": 209714
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 16,
  "_devurl": "https://github.com/jdstorey/edge",
  "_searchresults": 94,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/edge.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/storeylab/edge",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "apply_qvalue",
    "apply_sva",
    "betaCoef",
    "build_models",
    "build_study",
    "deSet",
    "fit_models",
    "fitFull",
    "fitNull",
    "fullMatrix",
    "fullMatrix<-",
    "fullModel",
    "fullModel<-",
    "individual",
    "individual<-",
    "kl_clust",
    "lrt",
    "nullMatrix",
    "nullMatrix<-",
    "nullModel",
    "nullModel<-",
    "odp",
    "qvalueObj",
    "qvalueObj<-",
    "resFull",
    "resNull",
    "show",
    "sType",
    "summary"
  ],
  "_datasets": [
    {
      "name": "endotoxin",
      "title": "Gene expression dataset from Calvano et al. (2005) Nature",
      "object": "endotoxin",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "gibson",
      "title": "Gene expression dataset from Idaghdour et al. (2008)",
      "object": "gibson",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "kidney",
      "title": "Gene expression dataset from Rodwell et al. (2004)",
      "object": "kidney",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "apply_qvalue",
      "title": "Estimate the q-values for a given set of p-values",
      "topics": [
        "apply_qvalue",
        "apply_qvalue,deSet-method"
      ]
    },
    {
      "page": "apply_sva",
      "title": "Estimate surrogate variables",
      "topics": [
        "apply_sva",
        "apply_sva,deSet-method"
      ]
    },
    {
      "page": "betaCoef",
      "title": "Regression coefficients from full model fit",
      "topics": [
        "betaCoef",
        "betaCoef,deFit-method"
      ]
    },
    {
      "page": "build_models",
      "title": "Generate a deSet object with full and null models",
      "topics": [
        "build_models"
      ]
    },
    {
      "page": "build_study",
      "title": "Formulates the experimental models",
      "topics": [
        "build_study"
      ]
    },
    {
      "page": "deFit-class",
      "title": "The differential expression class for the model fits",
      "topics": [
        "deFit-class"
      ]
    },
    {
      "page": "deSet",
      "title": "Create a deSet object from an ExpressionSet",
      "topics": [
        "deSet",
        "deSet,ExpressionSet-method"
      ]
    },
    {
      "page": "deSet-class",
      "title": "The differential expression class (deSet)",
      "topics": [
        "deSet-class"
      ]
    },
    {
      "page": "edge",
      "title": "Extraction of Differential Gene Expression",
      "topics": [
        "edge-package",
        "edge"
      ]
    },
    {
      "page": "endotoxin",
      "title": "Gene expression dataset from Calvano et al. (2005) Nature",
      "topics": [
        "endotoxin"
      ]
    },
    {
      "page": "fit_models",
      "title": "Linear regression of the null and full models",
      "topics": [
        "fit_models",
        "fit_models,deSet-method"
      ]
    },
    {
      "page": "fitFull",
      "title": "Fitted data from the full model",
      "topics": [
        "fitFull",
        "fitFull,deFit-method"
      ]
    },
    {
      "page": "fitNull",
      "title": "Fitted data from the null model",
      "topics": [
        "fitNull",
        "fitNull,deFit-method"
      ]
    },
    {
      "page": "fullMatrix",
      "title": "Matrix representation of full model",
      "topics": [
        "fullMatrix",
        "fullMatrix,deSet-method",
        "fullMatrix<-",
        "fullMatrix<-,deSet-method"
      ]
    },
    {
      "page": "fullModel",
      "title": "Full model equation",
      "topics": [
        "fullModel",
        "fullModel,deSet-method",
        "fullModel<-",
        "fullModel<-,deSet-method"
      ]
    },
    {
      "page": "gibson",
      "title": "Gene expression dataset from Idaghdour et al. (2008)",
      "topics": [
        "gibson"
      ]
    },
    {
      "page": "individual",
      "title": "Individuals sampled in experiment",
      "topics": [
        "individual",
        "individual,deSet-method",
        "individual<-",
        "individual<-,deSet-method"
      ]
    },
    {
      "page": "kidney",
      "title": "Gene expression dataset from Rodwell et al. (2004)",
      "topics": [
        "kidney"
      ]
    },
    {
      "page": "kl_clust",
      "title": "Modular optimal discovery procedure (mODP)",
      "topics": [
        "kl_clust",
        "kl_clust,deSet,deFit-method",
        "kl_clust,deSet,missing-method"
      ]
    },
    {
      "page": "lrt",
      "title": "Performs F-test (likelihood ratio test using Normal likelihood)",
      "topics": [
        "lrt",
        "lrt,deSet,deFit-method",
        "lrt,deSet,missing-method"
      ]
    },
    {
      "page": "nullMatrix",
      "title": "Matrix representation of null model",
      "topics": [
        "nullMatrix",
        "nullMatrix,deSet-method",
        "nullMatrix<-",
        "nullMatrix<-,deSet-method"
      ]
    },
    {
      "page": "nullModel",
      "title": "Null model equation from deSet object",
      "topics": [
        "nullModel",
        "nullModel,deSet-method",
        "nullModel<-",
        "nullModel<-,deSet-method"
      ]
    },
    {
      "page": "odp",
      "title": "The optimal discovery procedure",
      "topics": [
        "odp",
        "odp,deSet,deFit-method",
        "odp,deSet,missing-method"
      ]
    },
    {
      "page": "qvalueObj",
      "title": "Access/set qvalue slot",
      "topics": [
        "qvalueObj",
        "qvalueObj,deSet-method",
        "qvalueObj<-",
        "qvalueObj<-,deSet-method"
      ]
    },
    {
      "page": "resFull",
      "title": "Residuals of full model fit",
      "topics": [
        "resFull",
        "resFull,deFit-method"
      ]
    },
    {
      "page": "resNull",
      "title": "Residuals of null model fit",
      "topics": [
        "resNull",
        "resNull,deFit-method"
      ]
    },
    {
      "page": "show",
      "title": "Show function for deFit and deSet",
      "topics": [
        "show",
        "show,deFit-method",
        "show,deSet-method"
      ]
    },
    {
      "page": "sType",
      "title": "Statistic type used in analysis",
      "topics": [
        "sType",
        "sType,deFit-method"
      ]
    },
    {
      "page": "summary",
      "title": "Summary of deFit and deSet",
      "topics": [
        "summary",
        "summary,deFit-method",
        "summary,deSet-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/edge/raw/HEAD/README.md",
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "edgeR",
    "farver",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "nlme",
    "openssl",
    "pkgconfig",
    "plyr",
    "png",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "sva",
    "sys",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "edge.Rnw",
      "filename": "edge.pdf",
      "title": "edge Package",
      "engine": "knitr::knitr",
      "headings": [
        "Introduction",
        "Citing this package",
        "Getting help",
        "Quick start guide",
        "Case study: static experiment",
        "Case study: independent time course experiment",
        "Case study: longitudinal time course experiment",
        "sva: Surrogate variable analysis",
        "qvalue: Estimate the q-values",
        "Advanced topic: Using the ExpressionSet object"
      ],
      "created": "2015-04-14 17:06:48",
      "modified": "2024-03-27 20:34:01",
      "commits": 4
    }
  ],
  "_score": 7.772468403053281,
  "_indexed": true,
  "_nocasepkg": "edge",
  "_universes": [
    "bioc",
    "jdstorey"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:45.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/62b2395c24e0a4ae717a524208a49826a1b3efba93218de93bc273755651acc0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:58.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/de088541d96c933c9f6e9a48e0e0d47a8e8335313725520a50d1702362ab315f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.45.0",
      "date": "2026-07-04T13:00:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/4c0c78812b9763e86cf3957f809781fbe011c0b8f55d39e74209606705ee6b7f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:51.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/d12fc8d6b707be8b296768c7e26d2d10d1fd07bea0fa600b8da0b7ce505e90c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.45.0",
      "date": "2026-07-04T12:58:18.000Z",
      "arch": "aarch64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/06c27a41f88ec777f36209f7cb4a7fb524f13e65bc0c1ad2bcd31e2e92c968e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:32.000Z",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/fd8a943fe669a5f57180fc3907887ff341ece8ecb1e9bdcac8a4db3372ee5fc8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.45.0",
      "date": "2026-07-04T12:58:35.000Z",
      "arch": "aarch64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/f4e3f5992d8319063de4768553107a1f36ab0cd7db8ca4e6f42f3313a36a8b79",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:24.000Z",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/a166422bfe8878692031c6ee399673a19943fcffc0f568b24e574ea46b806d96",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.45.0",
      "date": "2026-07-04T12:59:57.000Z",
      "arch": "emscripten",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/b3c48732d86a40f073005975083d4ec553076f0e854d74d6a169f9945fcd54c3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.45.0",
      "date": "2026-07-04T12:58:52.000Z",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/b0fbf747f0e0175e95c1380f6cb578c16d3ebc6a5d482a0c683d22cdbc575d80",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.45.0",
      "date": "2026-07-04T12:58:22.000Z",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/f1bd9c8b480c025743d9798f3e103da6dd7fb104423ab4dcf8adb9b5f00a0e97",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.45.0",
      "date": "2026-07-04T12:58:47.000Z",
      "arch": "x86_64",
      "commit": "92259f8fb42447d24cecc2a8b683f0f3d5fc24b6",
      "fileid": "https://r2.ropensci.org/12463455b164750b24c29a0d8b1d60851d0c8eeb92de7ec2515bbb72beccdc03",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28706815107"
    }
  ]
}