{
  "_id": "6a5206109b92047c28d53f2b",
  "Package": "bacon",
  "Type": "Package",
  "Title": "Controlling bias and inflation in association studies using the\nempirical null distribution",
  "Version": "1.41.0",
  "Authors@R": "c(person(\"Maarten\", \"van Iterson\",\nemail=\"mviterson@gmail.com\", role=\"cre\"), person(\"Erik\", \"van\nZwet\", role=\"ctb\"))",
  "Author": "Maarten van Iterson [aut, cre], Erik van Zwet [ctb]",
  "Maintainer": "Maarten van Iterson <mviterson@gmail.com>",
  "Description": "Bacon can be used to remove inflation and bias often\nobserved in epigenome- and transcriptome-wide association\nstudies. To this end bacon constructs an empirical null\ndistribution using a Gibbs Sampling algorithm by fitting a\nthree-component normal mixture on z-scores.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "biocViews": "ImmunoOncology, StatisticalMethod, Bayesian, Regression,\nGenomeWideAssociation, Transcriptomics, RNASeq,\nMethylationArray, BatchEffect, MultipleComparison",
  "RoxygenNote": "7.3.1",
  "Collate": "'BaconClass.R' 'BaconMethods.R' 'bacon.R' 'normmixture.R'",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:56 UTC",
  "RemoteUrl": "https://github.com/bioc/bacon",
  "RemoteRef": "HEAD",
  "RemoteSha": "97774126744f4c63f4504d6ed21b2e766b287ccc",
  "Packaged": {
    "Date": "2026-07-11 08:54:38 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "bacon_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/552efa611fc44994af1fc5f11df994d835177add8afca92cd41a10061e9c2546",
  "_filesize": 1662412,
  "_sha256": "552efa611fc44994af1fc5f11df994d835177add8afca92cd41a10061e9c2546",
  "_expires": "2026-10-19T08:59:58.000Z",
  "_created": "2026-07-11T08:54:38.000Z",
  "_published": "2026-07-11T09:00:00.515Z",
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593",
  "_status": "success",
  "_upstream": "https://github.com/bioc/bacon",
  "_commit": {
    "id": "97774126744f4c63f4504d6ed21b2e766b287ccc",
    "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": 1777380176
  },
  "_maintainer": {
    "name": "Maarten van Iterson",
    "email": "mviterson@gmail.com",
    "login": "mvaniterson",
    "description": "",
    "uuid": 10561514
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 86529854953,
      "time": 173,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8247033118"
    },
    {
      "job": 86529854977,
      "time": 182,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8247034292"
    },
    {
      "job": 86529854962,
      "time": 250,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8247042481"
    },
    {
      "job": 86529854996,
      "time": 189,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8247035431"
    },
    {
      "job": 86529855005,
      "time": 278,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8247046106"
    },
    {
      "job": 86529855027,
      "time": 96,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8247022740"
    },
    {
      "job": 86529855043,
      "time": 177,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8247033380"
    },
    {
      "job": 86529855028,
      "time": 114,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8247025065"
    },
    {
      "job": 86529854984,
      "time": 225,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8247039726"
    },
    {
      "job": 86529510350,
      "time": 295,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8247009785"
    },
    {
      "job": 86529854955,
      "time": 126,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8247026660"
    },
    {
      "job": 86529854965,
      "time": 155,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8247030613"
    },
    {
      "job": 86529854978,
      "time": 186,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8247034794"
    },
    {
      "job": 86529854970,
      "time": 209,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8247037535"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Depends"
    },
    {
      "package": "ellipse",
      "role": "Depends"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "statisticalmethod",
    "bayesian",
    "regression",
    "genomewideassociation",
    "transcriptomics",
    "rnaseq",
    "methylationarray",
    "batcheffect",
    "multiplecomparison"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 562,
    "source": "https://www.bioconductor.org/packages/stats/bioc/bacon"
  },
  "_mentions": 4,
  "_searchresults": 173,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bacon.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bacon",
    "bias",
    "dnormmix",
    "es",
    "estimates",
    "fit",
    "inflation",
    "meta",
    "plot",
    "plotnormmix",
    "posteriors",
    "pval",
    "rnormmix",
    "se",
    "topTable",
    "traces",
    "tstat"
  ],
  "_help": [
    {
      "page": "bacon",
      "title": "Gibbs sampler",
      "topics": [
        "bacon"
      ]
    },
    {
      "page": "Bacon-class",
      "title": "An S4 class container for storing Gibbs Sampler input and output",
      "topics": [
        "Bacon-class"
      ]
    },
    {
      "page": "bias-methods",
      "title": "Method to extract the estimated bias from the 'bacon'-object",
      "topics": [
        "bias",
        "bias,Bacon-method"
      ]
    },
    {
      "page": "dnormmix",
      "title": "density of a k-component normal mixture",
      "topics": [
        "dnormmix"
      ]
    },
    {
      "page": "es-methods",
      "title": "Method to extract inflation- and bias-corrected effect-sizes",
      "topics": [
        "es",
        "es,Bacon-method"
      ]
    },
    {
      "page": "estimates-methods",
      "title": "Method to extract the estimated parameters from the 'bacon'-object",
      "topics": [
        "estimates",
        "estimates,Bacon-method"
      ]
    },
    {
      "page": "fit-methods",
      "title": "Method to plot mixture fit",
      "topics": [
        "fit",
        "fit,Bacon-method"
      ]
    },
    {
      "page": "inflation-methods",
      "title": "Method to extract the estimated inflation from the 'bacon'-object",
      "topics": [
        "inflation",
        "inflation,Bacon-method"
      ]
    },
    {
      "page": "meta-methods",
      "title": "fixed meta-analysis",
      "topics": [
        "meta",
        "meta,Bacon-method"
      ]
    },
    {
      "page": "plot-Bacon-method",
      "title": "plot hist or qq",
      "topics": [
        "plot,Bacon-method"
      ]
    },
    {
      "page": "plotnormmix",
      "title": "plot normal mixtures",
      "topics": [
        "plotnormmix"
      ]
    },
    {
      "page": "posteriors-methods",
      "title": "Method to plot posterior distribution",
      "topics": [
        "posteriors",
        "posteriors,Bacon-method"
      ]
    },
    {
      "page": "pval-methods",
      "title": "Method to extract inflation- and bias-corrected P-values",
      "topics": [
        "pval",
        "pval,Bacon-method"
      ]
    },
    {
      "page": "rnormmix",
      "title": "sample from a normal mixture",
      "topics": [
        "rnormmix"
      ]
    },
    {
      "page": "se-methods",
      "title": "Method to extract inflation- and bias-corrected standard errors",
      "topics": [
        "se",
        "se,Bacon-method"
      ]
    },
    {
      "page": "topTable-methods",
      "title": "topTable",
      "topics": [
        "topTable",
        "topTable,Bacon-method"
      ]
    },
    {
      "page": "traces-methods",
      "title": "Method to plot Gibbs sampling traces",
      "topics": [
        "traces",
        "traces,Bacon-method"
      ]
    },
    {
      "page": "tstat-methods",
      "title": "Method to extract inflation- and bias-corrected test-statistics",
      "topics": [
        "tstat",
        "tstat,Bacon-method"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "ellipse",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lambda.r",
    "lifecycle",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "snow",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "bacon.Rmd",
      "filename": "bacon.html",
      "title": "Controlling bias and inflation in association studies using the empirical null distribution",
      "author": "Maarten van Iterson [aut, cre] and Erik van Zwet [ctb]",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "A single set of test-statistics",
        "Multiple sets of test-statistics",
        "Fixed-effect meta-analysis",
        "Adjustment with 95% CI",
        "Session Info",
        "References"
      ],
      "created": "2016-03-17 00:22:39",
      "modified": "2024-04-17 16:58:50",
      "commits": 6
    }
  ],
  "_score": 5.141136090120739,
  "_indexed": true,
  "_nocasepkg": "bacon",
  "_universes": [
    "bioc",
    "mvaniterson"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-11T08:57:31.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/d1dbb27ebfb0d30e0ecd41b27096dab5bad5c407e9e5be644552a4e4dfd59ae1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-11T08:58:27.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/b07f080359b7ff052a547224059bc61036dd1d5cdee37b09e71c44194b81983c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-11T08:57:30.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/ee3653644c45a540d3f0a5f3b17c604fe8c1fcd7f3a9a131466a23f3520b6530",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-11T08:58:54.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/b47eb4616558ebceffa1815e8423c56ac48f39bbbb44cb4e81b6b1428d42115e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-11T08:56:02.000Z",
      "arch": "aarch64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/f59a6977b55f8630b7d812817a8362a434e74a5e8c50d526019560ce5b0861a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-11T08:57:04.000Z",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/863be848b23c9db6cc338943f06c76f80308ac22a4eb2f5ef72bfce210299cbb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-11T08:56:12.000Z",
      "arch": "aarch64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/b301c3b847c0aa85f7e170b39c94fd89f7eb1242fba86121133518782e7a7445",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-11T08:57:39.000Z",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/68a1a36b3d7c925bcbd0b4f49bc54f984af26a8ff5f1cdf940412709dac6d850",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-07-11T08:57:02.000Z",
      "arch": "emscripten",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/478861cfd8a110c91d7dd43a2a444569d2ca971e42df8c3c3cf0e76f1a6de9f9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-11T08:56:05.000Z",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/14af4d117fd181b6ef911503a5e1000c5d748a7f101ccc369d6cb7398c04c4cb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-11T08:56:25.000Z",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/d0e800d5747f383ca67302798d8fba17958872582f2c5749ffe122df1fe8f37a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-11T08:56:37.000Z",
      "arch": "x86_64",
      "commit": "97774126744f4c63f4504d6ed21b2e766b287ccc",
      "fileid": "https://r2.ropensci.org/bb65db8b2e70e443175876ac8605eb6d9081d5c882895f288720633927067811",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29146733593"
    }
  ]
}