{ "_id": "6a1ad87d1d7bb097a09e6c5c", "Package": "CNVMetrics", "Type": "Package", "Version": "1.17.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:57:34 UTC", "RemoteUrl": "https://github.com/bioc/CNVMetrics", "RemoteRef": "HEAD", "RemoteSha": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:53:33 UTC", "User": "root" }, "Author": "Astrid Deschênes [aut, cre] (ORCID:\n),\nPascal Belleau [aut] (ORCID: ),\nDavid A. Tuveson [aut] (ORCID: ),\nAlexander Krasnitz [aut]", "Maintainer": "Astrid Deschênes ", "MD5sum": "eb4c2e873a411352d641a0bf28649257", "_user": "bioc", "_type": "src", "_file": "CNVMetrics_1.17.0.tar.gz", "_fileid": "b561c2401ef4b496bbfd8b5cb3d550cc322fd3c2ca33c2e105b35414be1b33b8", "_filesize": 4905401, "_sha256": "b561c2401ef4b496bbfd8b5cb3d550cc322fd3c2ca33c2e105b35414be1b33b8", "_created": "2026-05-30T08:53:33.000Z", "_published": "2026-05-30T12:30:53.626Z", "_jobs": [ { "job": 78637910819, "time": 157, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306992251" }, { "job": 78637910824, "time": 238, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307000802" }, { "job": 78637910841, "time": 245, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307001472" }, { "job": 78637910831, "time": 127, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308178900" }, { "job": 78637910820, "time": 115, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308177595" }, { "job": 78637713774, "time": 215, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306975660" }, { "job": 78637910828, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306988645" }, { "job": 78637910842, "time": 160, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306992622" }, { "job": 78637910843, "time": 202, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306996746" }, { "job": 78637910826, "time": 161, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306992742" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CNVMetrics", "_commit": { "id": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": true, "_usedby": 0, "_updates": [ { "week": "2025-45", "n": 8 }, { "week": "2026-01", "n": 6 }, { "week": "2026-18", "n": 2 } ], "_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": 352, "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/HEAD/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": true, "_nocasepkg": "cnvmetrics", "_universes": [ "bioc", "adeschen", "krasnitzlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:56:41.000Z", "distro": "noble", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "eb327e60f87e27bfcee34d549742bfabfbd6bb0af6cf1c65df8b760a603364ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T08:56:47.000Z", "distro": "noble", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "9c9fbebe394d13b2d79714a3f2b99c2f58baf48811afc8db4bbb2e49b707d6fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-05-30T12:29:48.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "4a97f28d2f60cf31b529970b8cf0df042190feecbdc6eb4ebd6164653deb8bf1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.6.0", "os": "mac", "version": "1.17.0", "date": "2026-05-30T12:29:34.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "d3e0e99915306f7c1f6bcebc2e445b291ead521d8e304d7e012d8f82d3bfc210", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-05-30T08:55:56.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "679bd88d3aab1a4353d2e7b532e8be60ea2fbee42babb7f63e84011e7c3e5f2b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:55:11.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "41f1a57a05e57c7f0fd459981e668e3795335fcc974daf25c3f57606358374fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:55:38.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "a05c49325e36672d5064ac59120d72cf591b0fc71edc385aef28a920bcc3c8f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" }, { "r": "4.6.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T08:55:07.000Z", "commit": "39112e8a1955ccd1c9a9080094a2c50078cd0b99", "fileid": "bf5c72888a792038473c7b58273cbbec6c7b37612da4c626a5680d3fa722c1dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679657868" } ] }