{
  "_id": "6ae5d20595ca2370cc8d1a41",
  "Package": "dyebias",
  "Title": "The GASSCO method for correcting for slide-dependent\ngene-specific dye bias",
  "Version": "1.73.0",
  "Date": "2 March 2016",
  "Author": "Philip Lijnzaad and Thanasis Margaritis",
  "Description": "Many two-colour hybridizations suffer from a dye bias that\nis both gene-specific and slide-specific. The former depends on\nthe content of the nucleotide used for labeling; the latter\ndepends on the labeling percentage. The slide-dependency was\nhitherto not recognized, and made addressing the artefact\nimpossible.  Given a reasonable number of dye-swapped pairs of\nhybridizations, or of same vs. same hybridizations, both the\ngene- and slide-biases can be estimated and corrected using the\nGASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009),\ndoi:10.1038/msb.2009.21)",
  "Maintainer": "Philip Lijnzaad <plijnzaad@gmail.com>",
  "License": "GPL-3",
  "URL": "http://www.holstegelab.nl/publications/margaritis_lijnzaad",
  "biocViews": "Microarray, TwoChannel, QualityControl, Preprocessing",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:49 UTC",
  "RemoteUrl": "https://github.com/bioc/dyebias",
  "RemoteRef": "HEAD",
  "RemoteSha": "2344221e76264971831dee33405e81dba36698ec",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-31 10:27:53 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "dyebias_1.73.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/11a13b82b96eedfb92042ad4ec25098d404167611ba920cc7a85522960bd6440",
  "_filesize": 2802095,
  "_sha256": "11a13b82b96eedfb92042ad4ec25098d404167611ba920cc7a85522960bd6440",
  "_expires": "2027-02-08T11:33:23.000Z",
  "_created": "2026-10-31T10:27:53.000Z",
  "_published": "2026-10-31T11:33:25.730Z",
  "_upstream": "https://github.com/bioc/dyebias",
  "_status": "success",
  "_maintainer": {
    "name": "Philip Lijnzaad",
    "email": "plijnzaad@gmail.com",
    "login": "plijnzaad",
    "description": "works at the Princess Maxima Centre for Pediatric Oncology, Utrecht, Holland.",
    "uuid": 11426231
  },
  "_jobs": [
    {
      "job": 124513071399,
      "time": 139,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "13039527553"
    },
    {
      "job": 124513071429,
      "time": 196,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13039727122"
    },
    {
      "job": 124513071505,
      "time": 216,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "13039412160"
    },
    {
      "job": 124513071481,
      "time": 149,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13041102525"
    },
    {
      "job": 124513071466,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13041520061"
    },
    {
      "job": 124511537101,
      "time": 203,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13039262232"
    },
    {
      "job": 124513071482,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13039697099"
    },
    {
      "job": 124513071504,
      "time": 81,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13040105551"
    },
    {
      "job": 124513071507,
      "time": 114,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13039507594"
    },
    {
      "job": 124513071510,
      "time": 82,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13039706945"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 4,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257",
  "_commit": {
    "id": "2344221e76264971831dee33405e81dba36698ec",
    "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": 1777379629
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 1.4.1",
      "role": "Depends"
    },
    {
      "package": "marray",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "convert",
      "role": "Suggests"
    },
    {
      "package": "GEOquery",
      "role": "Suggests"
    },
    {
      "package": "dyebiasexamples",
      "role": "Suggests"
    },
    {
      "package": "methods",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.73.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.72.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microarray",
    "twochannel",
    "qualitycontrol",
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 480,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 722,
    "source": "https://www.bioconductor.org/packages/stats/bioc/dyebias"
  },
  "_mentions": 1,
  "_searchresults": 14,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/dyebias.html",
    "extra/manual.pdf",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "dyebias.application.subset",
    "dyebias.apply.correction",
    "dyebias.boxplot",
    "dyebias.estimate.iGSDBs",
    "dyebias.maplot",
    "dyebias.monotonicity",
    "dyebias.monotonicityplot",
    "dyebias.rgplot",
    "dyebias.trendplot"
  ],
  "_help": [
    {
      "page": "dyebias-package",
      "title": "The GASSCO method for correcting for slide-dependent gene-specific dye bias",
      "topics": [
        "dyebias-package",
        "dyebias"
      ]
    },
    {
      "page": "dyebias.application.subset",
      "title": "Return a subset of reporters that can be dye bias-corrected reasonably well",
      "topics": [
        "dyebias.application.subset"
      ]
    },
    {
      "page": "dyebias.apply.correction",
      "title": "Perform dye bias correction using the GASSCO method",
      "topics": [
        "dyebias.apply.correction"
      ]
    },
    {
      "page": "dyebias.boxplot",
      "title": "Creates boxplots of the reporters with the strongest dye bias",
      "topics": [
        "dyebias.boxplot"
      ]
    },
    {
      "page": "dyebias.estimate.iGSDBs",
      "title": "Estimate intrinsic gene specific dye biases (part of the GASSCO method)",
      "topics": [
        "dyebias.estimate.iGSDBs"
      ]
    },
    {
      "page": "dyebias.monotonicity",
      "title": "Calculate the degree of monotonicity of the dye bias across the slides. DEPRACATED",
      "topics": [
        "dyebias.monotonicity"
      ]
    },
    {
      "page": "dyebias.monotonicityplot",
      "title": "Show the degree of monotonicity of the dye bias across the slides. DEPRACATED",
      "topics": [
        "dyebias.monotonicityplot"
      ]
    },
    {
      "page": "dyebias.rgplot",
      "title": "Produce scatterplots of the hybridization, with strongest dye biases highlighted.",
      "topics": [
        "dyebias.maplot",
        "dyebias.rgplot"
      ]
    },
    {
      "page": "dyebias.trendplot",
      "title": "Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias.",
      "topics": [
        "dyebias.trendplot"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "limma",
    "marray",
    "statmod"
  ],
  "_vignettes": [
    {
      "source": "dyebias-vignette.Rnw",
      "filename": "dyebias-vignette.pdf",
      "title": "dye bias correction",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Installing",
        "Tuteja et al. (2008)",
        "Chen et al. (2007)",
        "Closing remarks",
        "sessionInfo"
      ],
      "created": "2013-11-01 20:08:03",
      "modified": "2018-09-06 15:51:07",
      "commits": 3
    }
  ],
  "_score": 3.4471580313422194,
  "_indexed": true,
  "_nocasepkg": "dyebias",
  "_universes": [
    "bioc",
    "plijnzaad"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-10-31T10:30:55.000Z",
      "distro": "resolute",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/1652e00efff20cc78da379242278530b1d45cb36b9815a0e919e3cdf4f6f0a69",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-10-31T10:31:22.000Z",
      "distro": "resolute",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/6e5cb7a40c6732f4a033003183852040fe0ed88c4d6678df6efc20e75ec31340",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-10-31T11:32:28.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/6b086a2e832f847ecf422d66ef1099d843c21e9421cadc76493c7cd4133bd4de",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-10-31T11:32:17.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/1efb5e783d0eff7ba680c5dd3fd4462cc9b048f3cc581958ce79da3e15a2342e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.73.0",
      "date": "2026-10-31T10:29:59.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/47f2534150c680a59fde38724c17d869d640c80c1b04b313b3136f0037d600da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-31T10:29:06.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/2a9b0843bb8410928e4b27650b94d9ff5552798b13b73b4643c8d89e7ed0739c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-31T10:29:32.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/951acfa3f0d9006258c28df60f8548f48a43bb0c62f339f21d16b90e0ab44425",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-10-31T10:29:07.000Z",
      "commit": "2344221e76264971831dee33405e81dba36698ec",
      "fileid": "https://r2.ropensci.org/d8e692a9b1faaff09b14c4515ad4c1af7ea9e2f544a7d5a083ff62d6f56dd7de",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192182257"
    }
  ]
}