{
  "_id": "6ace000ba14063b82c3ae42f",
  "Package": "cghMCR",
  "Version": "1.70.0",
  "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": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:31:44 UTC",
  "RemoteUrl": "https://github.com/bioc/cghMCR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-13 09:36:52 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "cghMCR_1.70.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c9c78c3dfdcf2b53ef3c8e3c728f2bff0479290a614c91efccfd92905b072d81",
  "_filesize": 38482809,
  "_sha256": "c9c78c3dfdcf2b53ef3c8e3c728f2bff0479290a614c91efccfd92905b072d81",
  "_expires": "2027-01-21T09:55:20.000Z",
  "_created": "2026-10-13T09:36:52.000Z",
  "_published": "2026-10-13T09:55:23.547Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 15
  },
  "_upstream": "https://github.com/bioc/cghMCR",
  "_commit": {
    "id": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
    "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": 1777379504
  },
  "_maintainer": {
    "name": "J. Zhang",
    "email": "jzhang@jimmy.harvard.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115230227963,
      "time": 144,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11801754190"
    },
    {
      "job": 115230227910,
      "time": 307,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11802465555"
    },
    {
      "job": 115230227740,
      "time": 308,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11802116719"
    },
    {
      "job": 115230227840,
      "time": 162,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11802427698"
    },
    {
      "job": 115230227852,
      "time": 188,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11802382905"
    },
    {
      "job": 115228491623,
      "time": 258,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11801109727"
    },
    {
      "job": 115230227836,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11802400106"
    },
    {
      "job": 115230227945,
      "time": 189,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11802126336"
    },
    {
      "job": 115230227856,
      "time": 181,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11801764266"
    },
    {
      "job": 115230227979,
      "time": 185,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11802355398"
    }
  ],
  "_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": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_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",
    "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": false,
  "_nocasepkg": "cghmcr",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/cghMCR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.70.0",
      "date": "2026-10-13T09:41:16.000Z",
      "distro": "resolute",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/1f2eaa474a7493035963deeb41fd3f6550991ba0980f2907394a71bb5c02e529",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.70.0",
      "date": "2026-10-13T09:41:21.000Z",
      "distro": "resolute",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/8aff2e3384096f29b56b0c1222f43666ae6d75eeb0b9bd38cc00c7f3ac82927e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.70.0",
      "date": "2026-10-13T09:53:28.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/ffd3fe8f8620cc1baa88c4008ee8254a6b8da57f0089962655273ebe7a166958",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.70.0",
      "date": "2026-10-13T09:53:14.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/d599f0f135a6d8ec4edb9f7d6c07eef953bb3393679b27873b18f327e97a7490",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.70.0",
      "date": "2026-10-13T09:39:54.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/8f78ff0d8980d3ffbc9af96e0b44785469e40911d0d05d9286e29a1b8717f6b0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-10-13T09:39:05.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/b51accfa90a0aa38a566435ac4f348cafdea59e6b73d337248dcba50182b4265",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-10-13T09:39:11.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/fc6c615538ff67e1e4ea6e701dea9f3edd38eba35c204df99352092ce96dba03",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.70.0",
      "date": "2026-10-13T09:39:08.000Z",
      "commit": "e1b9e56e897fdc4f082724cef8f736f6e0034904",
      "fileid": "https://r2.ropensci.org/dd12f1ccd6fb56721f96ca648fa8b69b631062050ad952df22f653e1299c2c44",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38377169062"
    }
  ]
}