{
  "_id": "6a49441018cdde069385ef37",
  "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": "2026-07-04 14:10:50 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "cghMCR_1.71.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/1964ae56decc461c0c08d2d4117cd794f8e9138a95c5a5e0e1bc87f537f57140",
  "_filesize": 38482002,
  "_sha256": "1964ae56decc461c0c08d2d4117cd794f8e9138a95c5a5e0e1bc87f537f57140",
  "_expires": "2026-10-12T17:34:00.000Z",
  "_created": "2026-07-04T14:10:50.000Z",
  "_published": "2026-07-04T17:34:07.980Z",
  "_bioccheck": {
    "error": 1,
    "warning": 5,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357",
  "_status": "success",
  "_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": 85152613606,
      "time": 176,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8082436011"
    },
    {
      "job": 85152613564,
      "time": 254,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8082444577"
    },
    {
      "job": 85152613555,
      "time": 249,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8082444278"
    },
    {
      "job": 85152613575,
      "time": 165,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8082434708"
    },
    {
      "job": 85152613580,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8082432661"
    },
    {
      "job": 85152613560,
      "time": 256,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082416273"
    },
    {
      "job": 85152613666,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8082433440"
    },
    {
      "job": 85152613543,
      "time": 179,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8082436257"
    },
    {
      "job": 85152613546,
      "time": 182,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8082436694"
    },
    {
      "job": 85152613667,
      "time": 169,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8082435212"
    }
  ],
  "_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"
    },
    {
      "branch": "release",
      "version": "1.70.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "copynumbervariation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_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",
    "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",
    "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": "2026-07-04T14:14:23.000Z",
      "distro": "resolute",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/1b47648abbc6df473d04a5fae86f63331ffe1e0ff28c4a496740a827815b15a1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.71.0",
      "date": "2026-07-04T14:14:26.000Z",
      "distro": "resolute",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/b01b8602144524d001424a133477431742824929c84c3c88bf5358e064626ad4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.71.0",
      "date": "2026-07-04T14:13:23.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/ef70d6ead757cd2c32997c108ef0e2e7841f9160f4cc72fff7b4a53ed8613221",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.71.0",
      "date": "2026-07-04T14:13:14.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/ee0d748ab32f705f57ccf2efcfefb79fb18e78c69ae38d348eaa35403afa30b5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.71.0",
      "date": "2026-07-04T14:14:04.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/180ae2d08b4b2c401dbae627d0190d0c1773e587f5afd5f8cdab7c01a713c26e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-07-04T14:13:04.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/9bdd6b0e9a9b4f25a07bf1de4a4f7278c0383f80353318b9ce7f7a84d68e85f8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-07-04T14:13:06.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/06882cdd55c97c5678c87ab6b47269816c5319d7a9a1fd21d41f605b048a4ad0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.71.0",
      "date": "2026-07-04T14:12:54.000Z",
      "commit": "aafc41391af90d657372461cb19f3504f85fc292",
      "fileid": "https://r2.ropensci.org/7e9da37f6ccc9defdb1d7d91ae915f33b9fb59079cd4a829ea1c558ce09944ff",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708720357"
    }
  ]
}