{
  "_id": "6aca772cfe5cc25786e89a6b",
  "Package": "cghMCR",
  "Version": "1.71.0",
  "Title": "Find chromosome regions showing common gains/losses",
  "Author": "J. Zhang and B. Feng",
  "Maintainer": "J. Zhang <jzhang@jimmy.harvard.edu>",
  "Description": "This package provides functions to identify genomic\nregions of interests based on segmented copy number data from\nmultiple samples.",
  "Keyword": "arrayCGH",
  "License": "LGPL",
  "LazyLoad": "yes",
  "biocViews": "Microarray, CopyNumberVariation",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:44 UTC",
  "RemoteUrl": "https://github.com/bioc/cghMCR",
  "RemoteRef": "HEAD",
  "RemoteSha": "aafc41391af90d657372461cb19f3504f85fc292",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 16:01:11 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "cghMCR_1.71.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/afff969416cd0bcc57a95f3af1643aefefc320c888b65a9f634a47e96b39b792",
  "_filesize": 38482566,
  "_sha256": "afff969416cd0bcc57a95f3af1643aefefc320c888b65a9f634a47e96b39b792",
  "_expires": "2027-01-18T17:34:31.000Z",
  "_created": "2026-10-10T16:01:11.000Z",
  "_published": "2026-10-10T17:34:35.873Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 2,
    "warning": 8,
    "note": 14
  },
  "_upstream": "https://github.com/bioc/cghMCR",
  "_commit": {
    "id": "aafc41391af90d657372461cb19f3504f85fc292",
    "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": 1777379504
  },
  "_maintainer": {
    "name": "J. Zhang",
    "email": "jzhang@jimmy.harvard.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114253756961,
      "time": 139,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11674963492"
    },
    {
      "job": 114253757003,
      "time": 305,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11674588051"
    },
    {
      "job": 114253757006,
      "time": 246,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11674433303"
    },
    {
      "job": 114253756929,
      "time": 163,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11677068463"
    },
    {
      "job": 114253757052,
      "time": 187,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11677405814"
    },
    {
      "job": 114252897896,
      "time": 255,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11674818428"
    },
    {
      "job": 114253756969,
      "time": 145,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11674423188"
    },
    {
      "job": 114253757072,
      "time": 176,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11674913803"
    },
    {
      "job": 114253756962,
      "time": 191,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11674108819"
    },
    {
      "job": 114253757040,
      "time": 183,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11674848705"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "DNAcopy",
      "role": "Depends"
    },
    {
      "package": "CNTools",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.1.6",
      "role": "Imports"
    },
    {
      "package": "stats4",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.71.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.70.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microarray",
    "copynumbervariation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 640,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cghMCR"
  },
  "_mentions": 15,
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cghMCR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cghMCR",
    "gol",
    "MCR",
    "mergeMCRProbes",
    "plot",
    "plot.DNAcopy",
    "SGOL"
  ],
  "_datasets": [
    {
      "name": "segData",
      "title": "The constructor for the cghMCR class",
      "object": "segData",
      "file": "segData.rda",
      "class": [
        "DNAcopy"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "cghMCR",
      "title": "The constructor for the cghMCR class",
      "topics": [
        "cghMCR",
        "segData"
      ]
    },
    {
      "page": "cghMCR-class",
      "title": "Class \"cghMCR\" is a S4 class for the identification of minimum common regions of gains or losses across samples",
      "topics": [
        "cghMCR-class",
        "getSegments",
        "getSegments,marrayNorm-method",
        "getSegments,marrayRaw-method",
        "MCR",
        "MCR,cghMCR-method"
      ]
    },
    {
      "page": "methods",
      "title": "Methods for Function colnames/rownames in Package `cghMCR'",
      "topics": [
        "colnames,SGOL-method",
        "colnames-methods",
        "rownames,SGOL-method",
        "rownames-methods",
        "[,SGOL-method",
        "[-methods"
      ]
    },
    {
      "page": "mergeMCRProbes",
      "title": "A function that appends probe ids to a data frame containing MCRs",
      "topics": [
        "mergeMCRProbes"
      ]
    },
    {
      "page": "plot.DNAcopy",
      "title": "A function to plot the original data along with the segments identified using segment of DNAcopy.",
      "topics": [
        "plot.DNAcopy"
      ]
    },
    {
      "page": "SGOL-class",
      "title": "Class \"SGOL\" reprents segments of gain or loss across samples",
      "topics": [
        "gol",
        "gol,SGOL-method",
        "method,SGOL-method",
        "plot",
        "plot,ANY-method",
        "plot,methods",
        "plot,SGOL,ANY-method",
        "plot,SGOL-method",
        "SGOL",
        "SGOL-class",
        "threshold,SGOL-method"
      ]
    }
  ],
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "CNTools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DNAcopy",
    "fastmap",
    "genefilter",
    "generics",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "limma",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "statmod",
    "survival",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "findMCR.Rnw",
      "filename": "findMCR.pdf",
      "title": "cghMCR findMCR",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "From raw to segmented data",
        "From raw data to segment list",
        "Identifying Segment Gain Or Loss (SGOL)",
        "Identifying Minimum Common Regions (MCR)",
        "Session Information",
        "References"
      ],
      "created": "2013-11-01 19:56:58",
      "modified": "2013-11-01 19:56:58",
      "commits": 1
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "cghmcr",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.71.0",
      "date": "2026-10-10T16:05:50.000Z",
      "distro": "resolute",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/516dd6abf76f0c910485c41d044fd4a6d6408bb166f847cb4a23f6c6fdd5f139",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.71.0",
      "date": "2026-10-10T16:05:02.000Z",
      "distro": "resolute",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/83b5fda95341806e364171f3e733e498a603287e33b54c1abd20b48ee2b268fa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.71.0",
      "date": "2026-10-10T17:31:48.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/d490981dbf4f4d2edca04f18928dd68c08f093fe04bbfe5bbc1fcea85331b846",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.71.0",
      "date": "2026-10-10T17:32:13.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/6778d70f2b13dbcd9a65cc107abbc26778e8edbd6b299e93eba5bf83073809f1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.71.0",
      "date": "2026-10-10T16:04:16.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/adc8b7fa6237edd79a21dab7a260550b89f98a91db1acc342c91d7b4d4660ad8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-10-10T16:03:14.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/c2ed972d9e27d35bd24472c84c93f39a1826b89d906306367badc2246fa0ab90",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-10-10T16:03:22.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/f4f02c95787221075a4dec596dec2de5f54f8305dca4eeaa991d5b54430e8755",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-10-10T16:03:29.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/f5fe7e7113f872431f412cbea24bab95e2e29ee99c59e19a00a806b2ca5e7217",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065722541"
    }
  ]
}