{
  "_id": "6abe548f99f7aa8c6aa556d9",
  "Package": "quantro",
  "Title": "A test for when to use quantile normalization",
  "Version": "1.46.0",
  "Authors@R": "c(\nperson(\"Stephanie\", \"Hicks\", role = c(\"aut\", \"cre\"),\nemail = \"shicks19@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-7858-0231\")),\nperson(\"Rafael\", \"Irizarry\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3944-4309\")))",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "6.0.1",
  "Encoding": "UTF-8",
  "Description": "A data-driven test for the assumptions of quantile\nnormalization using raw data such as objects that inherit eSets\n(e.g. ExpressionSet, MethylSet). Group level information about\neach sample (such as Tumor / Normal status) must also be\nprovided because the test assesses if there are global\ndifferences in the distributions between the user-defined\ngroups.",
  "License": "GPL-3",
  "biocViews": "Normalization, Preprocessing, MultipleComparison,\nMicroarray, Sequencing",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:39:34 UTC",
  "RemoteUrl": "https://github.com/bioc/quantro",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "63d0c19178934f2f770026e48f895e40ad44b241",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 12:10:28 UTC",
    "User": "root"
  },
  "Author": "Stephanie Hicks [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7858-0231>),\nRafael Irizarry [aut] (ORCID: <https://orcid.org/0000-0002-3944-4309>)",
  "Maintainer": "Stephanie Hicks <shicks19@jhu.edu>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "quantro_1.46.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/4433dd57e71025141a7d80e76e85e7ce8ef94dc352c8f7390eed2d984df7e027",
  "_filesize": 2719112,
  "_sha256": "4433dd57e71025141a7d80e76e85e7ce8ef94dc352c8f7390eed2d984df7e027",
  "_expires": "2027-01-09T12:39:41.000Z",
  "_created": "2026-10-01T12:10:28.000Z",
  "_published": "2026-10-01T12:39:43.736Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329",
  "_status": "success",
  "_upstream": "https://github.com/bioc/quantro",
  "_commit": {
    "id": "63d0c19178934f2f770026e48f895e40ad44b241",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379974
  },
  "_maintainer": {
    "name": "Stephanie Hicks",
    "email": "shicks19@jhu.edu",
    "login": "stephaniehicks",
    "linkedin": "in/hicksstephanie",
    "orcid": "0000-0002-7858-0231",
    "description": "Associate Professor in Biostatistics and Biomedical Engineering at Johns Hopkins University",
    "uuid": 1452065
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 110361941472,
      "time": 228,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11160603272"
    },
    {
      "job": 110361941269,
      "time": 719,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11160754508"
    },
    {
      "job": 110361941201,
      "time": 568,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11161028907"
    },
    {
      "job": 110361941180,
      "time": 359,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11162881648"
    },
    {
      "job": 110361941194,
      "time": 255,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11162731354"
    },
    {
      "job": 110359719813,
      "time": 376,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11161596470"
    },
    {
      "job": 110361941342,
      "time": 184,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11161547079"
    },
    {
      "job": 110361941214,
      "time": 418,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11161003583"
    },
    {
      "job": 110361941279,
      "time": 452,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11161342956"
    },
    {
      "job": 110361941273,
      "time": 396,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11161297899"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "minfi",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "normalization",
    "preprocessing",
    "multiplecomparison",
    "microarray",
    "sequencing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 471,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 867,
    "source": "https://www.bioconductor.org/packages/stats/bioc/quantro"
  },
  "_mentions": 6,
  "_searchresults": 233,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/quantro.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "anova",
    "matboxplot",
    "matdensity",
    "MSbetween",
    "MSwithin",
    "quantro",
    "quantroPlot",
    "quantroPvalPerm",
    "quantroStat",
    "quantroStatPerm",
    "summary"
  ],
  "_datasets": [
    {
      "name": "flowSorted",
      "title": "A subset of FlowSorted.DLPFC.450k data set",
      "object": "flowSorted",
      "file": "flowSorted.RData",
      "class": [
        "MethylSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "anova",
      "title": "Accessors for the 'anova' slot of a quantro object.",
      "topics": [
        "anova",
        "anova,quantro-method",
        "anova.quantro"
      ]
    },
    {
      "page": "flowSorted",
      "title": "A subset of FlowSorted.DLPFC.450k data set",
      "topics": [
        "flowSorted"
      ]
    },
    {
      "page": "matboxplot",
      "title": "Box plots of columns in a matrix",
      "topics": [
        "matboxplot"
      ]
    },
    {
      "page": "matdensity",
      "title": "Density plots of columns in a matrix",
      "topics": [
        "matdensity"
      ]
    },
    {
      "page": "MSbetween",
      "title": "Accessors for the 'MSbetween' slot of a quantro object.",
      "topics": [
        "MSbetween",
        "MSbetween,quantro-method",
        "MSbetween.quantro"
      ]
    },
    {
      "page": "MSwithin",
      "title": "Accessors for the 'MSwithin' slot of a quantro object.",
      "topics": [
        "MSwithin",
        "MSwithin,quantro-method",
        "MSwithin.quantro"
      ]
    },
    {
      "page": "quantro-class",
      "title": "quantro",
      "topics": [
        "quantro-class"
      ]
    },
    {
      "page": "quantroPlot",
      "title": "Plot results from 'quantro' function.",
      "topics": [
        "quantroPlot"
      ]
    },
    {
      "page": "quantroPvalPerm",
      "title": "Accessors for the 'quantroPvalPerm' slot of a quantro object.",
      "topics": [
        "quantroPvalPerm",
        "quantroPvalPerm,quantro-method",
        "quantroPvalPerm.quantro"
      ]
    },
    {
      "page": "quantroStat",
      "title": "Accessors for the 'quantroStat' slot of a quantro object.",
      "topics": [
        "quantroStat",
        "quantroStat,quantro-method",
        "quantroStat.quantro"
      ]
    },
    {
      "page": "quantroStatPerm",
      "title": "Accessors for the 'quantroStatPerm' slot of a quantro object.",
      "topics": [
        "quantroStatPerm",
        "quantroStatPerm,quantro-method",
        "quantroStatPerm.quantro"
      ]
    },
    {
      "page": "quantro",
      "title": "quantro",
      "topics": [
        "quantro",
        "show"
      ]
    },
    {
      "page": "summary",
      "title": "Accessors for the 'summary' slot of a quantro object.",
      "topics": [
        "summary",
        "summary,quantro-method",
        "summary.quantro"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/quantro/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64",
    "beanplot",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bumphunter",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "doParallel",
    "doRNG",
    "dplyr",
    "farver",
    "fastmap",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "ggplot2",
    "glue",
    "gtable",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "httr2",
    "illuminaio",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "mime",
    "minfi",
    "multtest",
    "nlme",
    "nor1mix",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "quadprog",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "rentrez",
    "reshape",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "scrime",
    "selectr",
    "Seqinfo",
    "siggenes",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "quantro.Rmd",
      "filename": "quantro.html",
      "title": "The quantro user's guide",
      "author": "Stephanie C. Hicks, Rafael Irizarry",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "Installation",
        "Load the package in R",
        "Data",
        "flowSorted Data Example",
        "Plot distributions",
        "Using the quantro() function",
        "Input for quantro()",
        "Running quantro()",
        "eSets",
        "Output from quantro()",
        "Assessing the statistical significance",
        "Visualizing the statistical significance from permutation tests",
        "SessionInfo"
      ],
      "created": "2019-03-31 19:02:25",
      "modified": "2021-06-18 16:36:32",
      "commits": 5
    }
  ],
  "_score": 6.923658421793307,
  "_indexed": false,
  "_nocasepkg": "quantro",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/quantro",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.46.0",
      "date": "2026-10-01T12:18:21.000Z",
      "distro": "resolute",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/ff93d47d79c26bd722ea2a1750bf92bacf92a2647ef910a859d603078e1a34f1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.46.0",
      "date": "2026-10-01T12:16:18.000Z",
      "distro": "resolute",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/6f33c559dfe30735c813ce0f9a07eaa9f49733eccc01b4f8e1af98c9c1753046",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.46.0",
      "date": "2026-10-01T12:34:48.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/0c42ca8d3ca52669ed2d1c9cf8873494291e57ecf6abe42b4ae37a7dbe7d0719",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.46.0",
      "date": "2026-10-01T12:33:48.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/3db3147b17ae63cf0be0f8103282a28d634eea9ae578302fc4d019ce377500b5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.46.0",
      "date": "2026-10-01T12:14:11.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/bf4b1d1bb8349b06ccb6d9fa844b79eac2c4d7e3d9bedf38b54898e6b5d3a07f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.46.0",
      "date": "2026-10-01T12:12:40.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/584d303043736fdcb2943ceca80926e926521300cc5aa3b44c5282594836b20a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.46.0",
      "date": "2026-10-01T12:13:16.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/be6f8a0e2350631929dca78f10d3387c3d4a25f8f845a5a8e84d753968ae529f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.46.0",
      "date": "2026-10-01T12:12:48.000Z",
      "commit": "63d0c19178934f2f770026e48f895e40ad44b241",
      "fileid": "https://r2.ropensci.org/84667b2a063b8df4d531813d2e4571472f9393303bb71a08dc6ef44a66d1fa04",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36859273329"
    }
  ]
}