{ "_id": "6a155889acfb0bcc41d5eb70", "Package": "copynumber", "Title": "Segmentation of single- and multi-track copy number data by\npenalized least squares regression (with hg38 and mm10).", "Version": "1.29.0.9000", "Author": "Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.", "Maintainer": "Gro Nilsen ", "Description": "Penalized least squares regression is applied to fit\npiecewise constant curves to copy number data to locate genomic\nregions of constant copy number. Procedures are available for\nindividual segmentation of each sample, joint segmentation of\nseveral samples and joint segmentation of the two data tracks\nfrom SNP-arrays. Several plotting functions are available for\nvisualization of the data and the segmentation results.", "License": "Artistic-2.0", "LazyData": "yes", "BuildResaveData": "best", "biocViews": "aCGH, SNP, CopyNumberVariation, Genetics, Visualization", "URL": "https://github.com/igordot/copynumber", "RoxygenNote": "7.1.1", "Repository": "https://shixiangwang.r-universe.dev", "Date/Publication": "2023-04-10 03:13:38 UTC", "RemoteUrl": "https://github.com/ShixiangWang/copynumber", "RemoteRef": "HEAD", "RemoteSha": "2e31d59f558d5e3e44215da2f612707791e3f030", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 08:19:43 UTC", "User": "root" }, "MD5sum": "867f92dd23393cd4f2dc97a355866f9c", "_user": "shixiangwang", "_type": "src", "_file": "copynumber_1.29.0.9000.tar.gz", "_fileid": "9785cbcd7303f3c40babfcad006fe2c40f9dce5f132532cd701d1bf1b36f9ffa", "_filesize": 904571, "_sha256": "9785cbcd7303f3c40babfcad006fe2c40f9dce5f132532cd701d1bf1b36f9ffa", "_created": "2026-05-26T08:19:43.000Z", "_published": "2026-05-26T08:23:37.352Z", "_distro": "noble", "_jobs": [ { "job": 77834768795, "time": 159, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7212203038" }, { "job": 77834768724, "time": 183, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7212210499" }, { "job": 77834768742, "time": 132, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7212194470" }, { "job": 77834768680, "time": 106, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7212186443" }, { "job": 77834355318, "time": 161, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7212150850" }, { "job": 77834768689, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7212184689" }, { "job": 77834768800, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7212195433" }, { "job": 77834768829, "time": 138, "config": "windows-oldrel", "r": 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"_topics": [ "acgh", "snp", "copynumbervariation", "genetics", "visualization" ], "_stars": 21, "_contributors": [ { "user": "shixiangwang", "count": 14, "uuid": 25057508 } ], "_userbio": { "uuid": 25057508, "type": "user", "name": "Shixiang Wang (王诗翔)", "description": "形每万变，神唯守一。" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/copynumber" }, "_devurl": "https://github.com/igordot/copynumber", "_searchresults": 102, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/copynumber.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "aspcf", "callAberrations", "getGRangesFormat", "imputeMissing", "interpolate.pcf", "multipcf", "pcf", "pcfPlain", "plotAberration", "plotAllele", "plotChrom", "plotCircle", "plotFreq", "plotGamma", "plotGenome", "plotHeatmap", 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"X34529", "X34530", "X33951", "X33952", "X33953", "X33954" ], "rows": 7658, "table": true, "tojson": true } ], "_help": [ { "page": "aspcf", "title": "Allele-specific copy number segmentation.", "topics": [ "aspcf" ] }, { "page": "callAberrations", "title": "Call aberrations in segmented data", "topics": [ "callAberrations" ] }, { "page": "getGRangesFormat", "title": "Get segments on the GRanges format", "topics": [ "getGRangesFormat" ] }, { "page": "imputeMissing", "title": "Impute missing copy number values", "topics": [ "imputeMissing" ] }, { "page": "interpolate.pcf", "title": "Interpolation of pcf-estimates.", "topics": [ "interpolate.pcf" ] }, { "page": "lymphoma", "title": "3K aCGH data", "topics": [ "lymphoma" ] }, { "page": "micma", "title": "Subset of 244K aCGH data", "topics": [ "micma" ] }, { "page": "multipcf", "title": "Multi-sample copy number segmentation.", "topics": [ "multipcf" ] }, { "page": "pcf", "title": "Single-sample copy number segmentation.", "topics": [ "pcf" ] }, { "page": "pcfPlain", "title": "Plain single-sample copy number segmentation.", "topics": [ "pcfPlain" ] }, { "page": "plotAberration", "title": "Plot areas with copy number aberrations", "topics": [ "plotAberration" ] }, { "page": "plotAllele", "title": "Plot SNP data and/or aspcf segmentation results", "topics": [ "plotAllele" ] }, { "page": "plotChrom", "title": "Plot copy number data and/or segmentation results by chromosome", "topics": [ "plotChrom" ] }, { "page": "plotCircle", "title": "Plot a circular genome with aberration frequencies and connections between genomic loci added.", "topics": [ "plotCircle" ] }, { "page": "plotFreq", "title": "Plot percentage of samples with an aberration at a genomic position", "topics": [ "plotFreq" ] }, { "page": "plotGamma", "title": "Plot segmentation results for several values of gamma", "topics": [ "plotGamma" ] }, { "page": "plotGenome", "title": "Plot copy number data and/or segmentation results", "topics": [ "plotGenome" ] }, { "page": "plotHeatmap", "title": "Plot copy number heatmap", "topics": [ "plotHeatmap" ] }, { "page": "plotSample", "title": "Plot copy number data and/or segmentation results by sample", "topics": [ "plotSample" ] }, { "page": "selectSegments", "title": "Select multipcf segments", "topics": [ "selectSegments" ] }, { "page": "SNPdata", "title": "Artificial SNP array data", "topics": [ "BAF", "logR" ] }, { "page": "subsetData", "title": "Retrieve a data subset", "topics": [ "subsetData" ] }, { "page": "subsetSegments", "title": "Retrieve a subset of segments", "topics": [ "subsetSegments" ] }, { "page": "winsorize", "title": "Winsorization of copy number data", "topics": [ "winsorize" ] } ], "_readme": "https://github.com/ShixiangWang/copynumber/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "generics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo" ], "_score": 4.029789470831856, "_indexed": true, "_nocasepkg": "copynumber", "_universes": [ "shixiangwang", "igordot" ], 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