{
  "_id": "6a1ac43e1d7bb097a09db209",
  "Package": "marr",
  "Type": "Package",
  "Title": "Maximum rank reproducibility",
  "Version": "1.23.0",
  "Date": "2021-05-10",
  "Authors@R": "c(person(\"Tusharkanti\", \"Ghosh\",\nemail = \"tusharkantighosh30@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Max\", \"McGrath\",\nrole = c(\"aut\")),\nperson(\"Daisy\", \"Philtron\",\nrole = c(\"aut\")),\nperson(\"Katerina\", \"Kechris\",\nrole = c(\"aut\")),\nperson(\"Debashis\", \"Ghosh\",\nrole = c(\"aut\", \"cph\")))",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "License": "GPL (>= 3)",
  "Description": "marr (Maximum Rank Reproducibility) is a nonparametric\napproach that detects reproducible signals using a maximal rank\nstatistic for high-dimensional biological data. In this R\npackage, we implement functions that measures the\nreproducibility of features per sample pair and sample pairs\nper feature in high-dimensional biological replicate\nexperiments. The user-friendly plot functions in this package\nalso plot histograms of the reproducibility of features per\nsample pair and sample pairs per feature. Furthermore, our\napproach also allows the users to select optimal filtering\nthreshold values for the identification of reproducible\nfeatures and sample pairs based on output visualization checks\n(histograms). This package also provides the subset of data\nfiltered by reproducible features and/or sample pairs.",
  "biocViews": "QualityControl, Metabolomics, MassSpectrometry, RNASeq,\nChIPSeq",
  "BugReports": "https://github.com/Ghoshlab/marr/issues",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:24 UTC",
  "RemoteUrl": "https://github.com/bioc/marr",
  "RemoteRef": "HEAD",
  "RemoteSha": "d5696f797226f3446022164168e0db7e4a6b794e",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 07:43:49 UTC",
    "User": "root"
  },
  "Author": "Tusharkanti Ghosh [aut, cre],\nMax McGrath [aut],\nDaisy Philtron [aut],\nKaterina Kechris [aut],\nDebashis Ghosh [aut, cph]",
  "Maintainer": "Tusharkanti Ghosh <tusharkantighosh30@gmail.com>",
  "MD5sum": "766ccf3e6eb567e63a73858cb274774b",
  "_user": "bioc",
  "_type": "src",
  "_file": "marr_1.23.0.tar.gz",
  "_fileid": "56497bc63e7355305c79b7c84b958ed4c563100624140249c2e926e2d390f6f1",
  "_filesize": 497539,
  "_sha256": "56497bc63e7355305c79b7c84b958ed4c563100624140249c2e926e2d390f6f1",
  "_created": "2026-05-30T07:43:49.000Z",
  "_published": "2026-05-30T11:04:30.409Z",
  "_jobs": [
    {
      "job": 78634361059,
      "time": 179,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306587994"
    },
    {
      "job": 78634361095,
      "time": 250,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306595135"
    },
    {
      "job": 78634361079,
      "time": 338,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306603448"
    },
    {
      "job": 78634361088,
      "time": 252,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306595256"
    },
    {
      "job": 78634361078,
      "time": 325,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306602313"
    },
    {
      "job": 78634361091,
      "time": 163,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307714129"
    },
    {
      "job": 78634361089,
      "time": 501,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306621898"
    },
    {
      "job": 78634361082,
      "time": 243,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307719003"
    },
    {
      "job": 78634361063,
      "time": 375,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306612167"
    },
    {
      "job": 78634122703,
      "time": 284,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306570453"
    },
    {
      "job": 78634361061,
      "time": 146,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306584896"
    },
    {
      "job": 78634361066,
      "time": 278,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306597707"
    },
    {
      "job": 78634361070,
      "time": 233,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306593416"
    },
    {
      "job": 78634361080,
      "time": 246,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306594734"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/marr",
  "_commit": {
    "id": "d5696f797226f3446022164168e0db7e4a6b794e",
    "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": 1777380864
  },
  "_maintainer": {
    "name": "Tusharkanti Ghosh",
    "email": "tusharkantighosh30@gmail.com"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "qualitycontrol",
    "metabolomics",
    "massspectrometry",
    "rnaseq",
    "chipseq",
    "cpp"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "tghosh30",
      "count": 217,
      "uuid": 44294394
    },
    {
      "user": "max-mcgrath",
      "count": 8,
      "uuid": 49347694
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 322,
    "source": "https://www.bioconductor.org/packages/stats/bioc/marr"
  },
  "_devurl": "https://github.com/ghoshlab/marr",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/marr.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ghoshlab/marr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Marr",
    "MarrAlpha",
    "MarrData",
    "MarrFeatures",
    "MarrFeaturesfiltered",
    "MarrFeatureVars",
    "MarrFilterData",
    "MarrPFeatures",
    "MarrPlotFeatures",
    "MarrPlotSamplepairs",
    "MarrProc",
    "MarrPSamplepairs",
    "MarrSamplepairs",
    "MarrSamplepairsfiltered"
  ],
  "_datasets": [
    {
      "name": "msprepCOPD",
      "title": "Example of processed mass spectrometry dataset",
      "object": "msprepCOPD",
      "file": "msprepCOPD.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "data.frameORSummarizedExperiment-class",
      "title": "S4 Class union",
      "topics": [
        "data.frameORSummarizedExperiment-class"
      ]
    },
    {
      "page": "Marr",
      "title": "Marr",
      "topics": [
        "Marr"
      ]
    },
    {
      "page": "Marr-class",
      "title": "the Marr class",
      "topics": [
        "Marr-class"
      ]
    },
    {
      "page": "MarrAlpha",
      "title": "Generic function that returns the Marr Alpha",
      "topics": [
        "MarrAlpha",
        "MarrAlpha,Marr-method"
      ]
    },
    {
      "page": "MarrData",
      "title": "Generic function that returns the Marr Data",
      "topics": [
        "MarrData",
        "MarrData,Marr-method"
      ]
    },
    {
      "page": "MarrFeatures",
      "title": "Generic function that returns the Marr features",
      "topics": [
        "MarrFeatures",
        "MarrFeatures,Marr-method"
      ]
    },
    {
      "page": "MarrFeaturesfiltered",
      "title": "Generic function that returns the Marr filtered features",
      "topics": [
        "MarrFeaturesfiltered",
        "MarrFeaturesfiltered,Marr-method"
      ]
    },
    {
      "page": "MarrFeatureVars",
      "title": "Generic function that returns the Marr Feature Vars",
      "topics": [
        "MarrFeatureVars",
        "MarrFeatureVars,Marr-method"
      ]
    },
    {
      "page": "MarrFilterData",
      "title": "Filter by Maximum Rank Reproducibility",
      "topics": [
        "MarrFilterData"
      ]
    },
    {
      "page": "MarrPFeatures",
      "title": "Generic function that returns the Marr P Features",
      "topics": [
        "MarrPFeatures",
        "MarrPFeatures,Marr-method"
      ]
    },
    {
      "page": "MarrPlotFeatures",
      "title": "Plot percent reproducible sample pairs per feature for pairwise replicates from 'Marr' function.",
      "topics": [
        "MarrPlotFeatures"
      ]
    },
    {
      "page": "MarrPlotSamplepairs",
      "title": "Plot percent reproducible features per sample pair for pairwise replicates from 'Marr' function.",
      "topics": [
        "MarrPlotSamplepairs"
      ]
    },
    {
      "page": "MarrProc",
      "title": "MarrProc",
      "topics": [
        "MarrProc"
      ]
    },
    {
      "page": "MarrPSamplepairs",
      "title": "Generic function that returns the Marr P Sample Pairs",
      "topics": [
        "MarrPSamplepairs",
        "MarrPSamplepairs,Marr-method"
      ]
    },
    {
      "page": "MarrSamplepairs",
      "title": "Generic function that returns the Marr sample pairs",
      "topics": [
        "MarrSamplepairs",
        "MarrSamplepairs,Marr-method"
      ]
    },
    {
      "page": "MarrSamplepairsfiltered",
      "title": "Generic function that returns the Marr filtered sample pairs",
      "topics": [
        "MarrSamplepairsfiltered",
        "MarrSamplepairsfiltered,Marr-method"
      ]
    },
    {
      "page": "msprepCOPD",
      "title": "Example of processed mass spectrometry dataset",
      "topics": [
        "msprepCOPD"
      ]
    },
    {
      "page": "vectorORNull-class",
      "title": "S4 Class union",
      "topics": [
        "vectorORNull-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/marr/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "dplyr",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "MarrVignette.Rmd",
      "filename": "MarrVignette.html",
      "title": "The marr user's guide",
      "author": "Tusharkanti Ghosh, Max McGrath, Daisy Philtron, Katerina Kechris, Debashis Ghosh",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "msprepCOPD Data",
        "msprepCOPD data pre-processing",
        "Using the Marr() function",
        "Input for Marr()",
        "Running Marr()",
        "msprepCOPD SummarizedExperiment example - Evaluating reproducibility",
        "Filtering the data by reproducible features and/or sample pairs",
        "Session Info",
        "References"
      ],
      "created": "2020-10-23 06:26:40",
      "modified": "2021-04-28 00:57:47",
      "commits": 9
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": true,
  "_nocasepkg": "marr",
  "_universes": [
    "bioc",
    "ghoshlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:46:36.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "d16a6816be0758f1954db125468456576058390d2adb8b146372d3f53ae97626",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:47:27.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "2ef4e33bb9eeb890a128d075f5bbfb803f09c35b43536545358aa10c09c35782",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:46:38.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "87eba144dc9fcb827a2337a84e4d0a318f0b5c7618f3a5e2c5cc7cbdbc734793",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:47:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "b090488ce6d9af37d97472486f4594de2ef7c53ec6c19307a61664dfc2e55a6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T11:01:42.000Z",
      "arch": "aarch64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "35d9bc3c2a6daac4c5a3c66e7522fb721e436363586e28e4fb614f6efb98ab0e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T07:49:10.000Z",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "d8c67769120f9ba4c2b5be5143d7d9cb053dc997b099e6dcbf031373cc5df9a6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T11:01:50.000Z",
      "arch": "aarch64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "7e642216c4f8fcf0812e4904105ea988608ef99cb0d03adc38fcf86ccf3bcd0d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T07:47:59.000Z",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "7c07140b5002ed639f7ac1e8f687738175c911a270fa2061b0609425f289727f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-05-30T07:46:52.000Z",
      "arch": "emscripten",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "d4fabdca07f6a8bfc084a19d5166bcec692c432991f6c2e33b98a606e640a90e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:45:50.000Z",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "ebf34d123eec7e67bd1fe9c4bee8caa5f51169cf19ee4131854360df19c14584",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:45:41.000Z",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "b6d58b7c077b8a2982c38c049968c7285f565017e5e86e96f44547e8acde65c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:45:33.000Z",
      "arch": "x86_64",
      "commit": "d5696f797226f3446022164168e0db7e4a6b794e",
      "fileid": "229b856f96c3e9c4700615a73538b2316f224cbd61eb02449ecf280b97270310",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678297313"
    }
  ]
}