{
  "_id": "6a1fe059b401979e734394c0",
  "Package": "CNVMetrics",
  "Type": "Package",
  "Version": "1.16.0",
  "Date": "2021-11-23",
  "Title": "Copy Number Variant Metrics",
  "Description": "The CNVMetrics package calculates similarity metrics to\nfacilitate copy number variant comparison among samples and/or\nmethods. Similarity metrics can be employed to compare CNV\nprofiles of genetically unrelated samples as well as those with\na common genetic background. Some metrics are based on the\nshared amplified/deleted regions while other metrics rely on\nthe level of amplification/deletion. The data type used as\ninput is a plain text file containing the genomic position of\nthe copy number variations, as well as the status and/or the\nlog2 ratio values. Finally, a visualization tool is provided to\nexplore resulting metrics.",
  "Authors@R": "c(person(\"Astrid\", \"Deschênes\", email = \"adeschen@hotmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7846-6749\")),\nperson(\"Pascal\", \"Belleau\", email = \"pascal_belleau@hotmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-0802-1071\")),\nperson(given=\"David A.\", family=\"Tuveson\",\nemail=\"dtuveson@cshl.edu\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-8017-2712\")),\nperson(\"Alexander\", \"Krasnitz\", email = \"krasnitz@cshl.edu\",\nrole = c(\"aut\")))",
  "Encoding": "UTF-8",
  "License": "Artistic-2.0",
  "biocViews": "BiologicalQuestion, Software, CopyNumberVariation",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/krasnitzlab/CNVMetrics,\nhttps://krasnitzlab.github.io/CNVMetrics/",
  "BugReports": "https://github.com/krasnitzlab/CNVMetrics/issues",
  "RoxygenNote": "7.3.3",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:34 UTC",
  "RemoteUrl": "https://github.com/bioc/CNVMetrics",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 08:00:12 UTC",
    "User": "root"
  },
  "Author": "Astrid Deschênes [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7846-6749>),\nPascal Belleau [aut] (ORCID: <https://orcid.org/0000-0002-0802-1071>),\nDavid A. Tuveson [aut] (ORCID: <https://orcid.org/0000-0002-8017-2712>),\nAlexander Krasnitz [aut]",
  "Maintainer": "Astrid Deschênes <adeschen@hotmail.com>",
  "MD5sum": "40e02147ab35a446fd6844fa058060c2",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "CNVMetrics_1.16.0.tar.gz",
  "_fileid": "8203f31cac3ae8545259d444633580cde3b0d8e2df22ccd91ed3e57eeb25acb5",
  "_filesize": 4905459,
  "_sha256": "8203f31cac3ae8545259d444633580cde3b0d8e2df22ccd91ed3e57eeb25acb5",
  "_created": "2026-06-03T08:00:12.000Z",
  "_published": "2026-06-03T08:05:45.913Z",
  "_jobs": [
    {
      "job": 79248435535,
      "time": 214,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378964758"
    },
    {
      "job": 79248435837,
      "time": 282,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7378987826"
    },
    {
      "job": 79248435522,
      "time": 233,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378971461"
    },
    {
      "job": 79248435527,
      "time": 139,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7378939057"
    },
    {
      "job": 79248435515,
      "time": 169,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378949339"
    },
    {
      "job": 79247793498,
      "time": 235,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378890268"
    },
    {
      "job": 79248435495,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378937795"
    },
    {
      "job": 79248435615,
      "time": 170,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7378949849"
    },
    {
      "job": 79248435534,
      "time": 155,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7378944350"
    },
    {
      "job": 79248435617,
      "time": 160,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378946023"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CNVMetrics",
  "_commit": {
    "id": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
    "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": 1777381054
  },
  "_maintainer": {
    "name": "Astrid Deschênes",
    "email": "adeschen@hotmail.com",
    "login": "adeschen",
    "orcid": "0000-0001-7846-6749",
    "description": "I am a Computational Science Analyst at Cold Spring Harbor Laboratory. ",
    "uuid": 7254636
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "rBeta2009",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "XVector",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-45",
      "n": 8
    },
    {
      "week": "2026-01",
      "n": 6
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "biologicalquestion",
    "software",
    "copynumbervariation",
    "cnv",
    "copy-number-variation",
    "metrics",
    "r-language"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "adeschen",
      "count": 462,
      "uuid": 7254636
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "belleau",
      "count": 4,
      "uuid": 8398253
    },
    {
      "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": 310,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CNVMetrics"
  },
  "_devurl": "https://github.com/krasnitzlab/cnvmetrics",
  "_pkgdown": "https://krasnitzlab.github.io/CNVMetrics/",
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNVMetrics.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/krasnitzlab/cnvmetrics",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateLog2ratioMetric",
    "calculateOverlapMetric",
    "plotMetric",
    "processSim"
  ],
  "_help": [
    {
      "page": "CNVMetrics-package",
      "title": "CNVMetrics: Copy number variant metrics",
      "topics": [
        "CNVMetrics-package",
        "CNVMetrics"
      ]
    },
    {
      "page": "calculateLog2ratioMetric",
      "title": "Calculate metric using overlapping amplified/deleted regions",
      "topics": [
        "calculateLog2ratioMetric"
      ]
    },
    {
      "page": "calculateOverlapMetric",
      "title": "Calculate metric using overlapping amplified/deleted regions",
      "topics": [
        "calculateOverlapMetric"
      ]
    },
    {
      "page": "is.CNVMetric",
      "title": "Is an object of class 'CNVMetric'",
      "topics": [
        "is.CNVMetric"
      ]
    },
    {
      "page": "plotMetric",
      "title": "Plot metrics present in a 'CNVMetric' object",
      "topics": [
        "plotMetric"
      ]
    },
    {
      "page": "print.CNVMetric",
      "title": "Print CNVMetric object",
      "topics": [
        "print.CNVMetric"
      ]
    },
    {
      "page": "processSim",
      "title": "Generate simulated samples with copy number profiles derived from a specific sample",
      "topics": [
        "processSim"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CNVMetrics/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "gridExtra",
    "gtable",
    "IRanges",
    "labeling",
    "lambda.r",
    "lifecycle",
    "magrittr",
    "pheatmap",
    "R6",
    "rBeta2009",
    "RColorBrewer",
    "rlang",
    "S4Vectors",
    "scales",
    "Seqinfo",
    "snow",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "CNVMetrics.Rmd",
      "filename": "CNVMetrics.html",
      "title": "Quantifying similarity between copy number profiles",
      "author": "Astrid Deschênes, Pascal Belleau and Alexander Krasnitz",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Licensing",
        "Citing",
        "Introduction",
        "Installation",
        "Workflow for metrics calculated using CNV status calls",
        "Data Input - Copy number file containing the CNV status calls",
        "Data Importation - GRangesList",
        "Metric Calculation",
        "Metric Visualization",
        "Metrics using the CNV status calls",
        "Sørensen",
        "Szymkiewicz–Simpson",
        "Jaccard",
        "Workflow for metrics calculated using the level of amplification/deletion",
        "Data Input - Copy number file containing the level of amplification/deletion",
        "Metrics using the level of amplification/deletion",
        "Weighted Euclidean Distance-Based",
        "Copy number profile simulating method",
        "Supplementary information",
        "Using parallelization",
        "Creating your own GRangesList",
        "Reproducible research",
        "Acknowledgments",
        "Session info",
        "References"
      ],
      "created": "2018-08-24 03:08:31",
      "modified": "2022-10-20 22:53:41",
      "commits": 41
    }
  ],
  "_score": 5.2552725051033065,
  "_indexed": false,
  "_nocasepkg": "cnvmetrics",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/CNVMetrics",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.16.0",
      "date": "2026-06-03T08:04:08.000Z",
      "distro": "noble",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "d9c912cb4c6844b63f481bef7cf0775b6a2b41b2701a1c4d19475e2dcfb53730",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.16.0",
      "date": "2026-06-03T08:03:15.000Z",
      "distro": "noble",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "2e3fc8609f76f46a1928b16ff4c8776e7a0cfb0f36ff2a9faf1242931de2e5e8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.16.0",
      "date": "2026-06-03T08:02:09.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "da20b785a290bf2e0ae8689656e356fdd99e96d4b57534b23227c56dd8ea7c21",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.16.0",
      "date": "2026-06-03T08:02:22.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "3f79f0620919be515359d30631a37fd498eb7b5597e7b0c567e57219a1ebea8b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.16.0",
      "date": "2026-06-03T08:02:55.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "ea8309c941d1c22684b597369f43e5423abbc4683edfce63c4e902117be74c89",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-06-03T08:02:16.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "37f22b593d5a549b5f40ed99b07344afee2bbb67aa0e8bc398fa79e56db00bea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-06-03T08:01:53.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "3afb922195f3f92878c967d39da4814db5aa7109d94cd8cbec95582348dd2902",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-06-03T08:02:00.000Z",
      "commit": "2dfb3a77f4ab12a6122403d6374383d287b4eeb5",
      "fileid": "61aeb307da4ba3b0e36242b7efcb69f1f58238a0967149cd7d2052a70a6897a8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871516676"
    }
  ]
}