{ "_id": "6a1ad6b21d7bb097a09e5e41", "Package": "CNAnorm", "Version": "1.59.0", "Date": "2012-08-06", "Title": "A normalization method for Copy Number Aberration in cancer\nsamples", "Author": "Stefano Berri , Henry M. Wood\n, Arief Gusnanto ", "Maintainer": "Stefano Berri ", "Description": "Performs ratio, GC content correction and normalization of\ndata obtained using low coverage (one read every 100-10,000 bp)\nhigh troughput sequencing. It performs a \"discrete\"\nnormalization looking for the ploidy of the genome. It will\nalso provide tumour content if at least two ploidy states can\nbe found.", "License": "GPL-2", "Collate": "AllGenerics.R AllClasses.R dataFrame2object.R\nworkflowWrapper.R initialize-methods.R summary-methods.R\nsmoothseg.R bandsegment.R mixtureModel.R normalize.R\nlength-methods.R CNAnorm-accessors.R CNAnorm-methods.R\nData-methods.R makeDefaultGraphParamteres.R", "URL": "http://www.r-project.org,", "LazyLoad": "yes", "Packaged": { "Date": "2026-05-30 08:50:52 UTC", "User": "root" }, "biocViews": "CopyNumberVariation, Sequencing, Coverage, Normalization,\nWholeGenome, DNASeq, GenomicVariation", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:53 UTC", "RemoteUrl": "https://github.com/bioc/CNAnorm", "RemoteRef": "HEAD", "RemoteSha": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "NeedsCompilation": "yes", "MD5sum": "d17331b218a0a2e03532af7818e51d42", "_user": "bioc", "_type": "src", "_file": "CNAnorm_1.59.0.tar.gz", "_fileid": "4561748de0e9747ebf7d6538a645dee550b1b2a41a5839e6b11394a19d22e9f0", "_filesize": 1642000, "_sha256": "4561748de0e9747ebf7d6538a645dee550b1b2a41a5839e6b11394a19d22e9f0", "_created": "2026-05-30T08:50:52.000Z", "_published": "2026-05-30T12:23:14.659Z", "_jobs": [ { "job": 78637764236, "time": 130, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306972111" }, { "job": 78637764271, "time": 121, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306971021" }, { "job": 78637764261, "time": 181, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306977227" }, { "job": 78637764258, "time": 153, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306974504" }, { "job": 78637764260, "time": 161, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306975403" }, { "job": 78637764264, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308133569" }, { "job": 78637764273, "time": 228, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306982153" }, { "job": 78637764269, "time": 126, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308135572" }, { "job": 78637764266, "time": 295, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306993284" }, { "job": 78637603708, "time": 157, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306958303" }, { "job": 78637764229, "time": 87, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306967408" }, { "job": 78637764238, "time": 119, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306970765" }, { "job": 78637764240, "time": 126, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306971205" }, { "job": 78637764241, "time": 92, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306967880" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CNAnorm", "_commit": { "id": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379753 }, "_maintainer": { "name": "Stefano Berri", "email": "sberri@illumina.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.1", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "DNAcopy", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "sequencing", "coverage", "normalization", "wholegenome", "dnaseq", "genomicvariation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 421, "source": "https://www.bioconductor.org/packages/stats/bioc/CNAnorm" }, "_mentions": 21, "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNAnorm.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addDNACopy", "addSmooth", "arms", "chrs", "chrs<-", "CNAnormWorkflow", "dataFrame2object", "discreteNorm", "exportTable", "gcNorm", "peakPloidy", "plotGenome", "plotPeaks", "pos", "pos<-", "ratio", "ratio.n", "ratio.s", "ratio.s.n", "segMean", "segMean.n", "sugg.peaks", "sugg.ploidy", "valid.peaks", "valid.ploidy", "validation" ], "_datasets": [ { "name": "CN", "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.", "object": "CN", "file": "CN.RData", "class": [ "CNAnorm" ], "fields": [], "table": false, "tojson": false }, { "name": "gPar", "title": "An object with the default graphical parameters", "object": "gPar", "file": "gPar.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "hg19_hs_ideogr", "title": "An object with the ideogram information for homo sapiens - hg19", "object": "hg19_hs_ideogr", "file": "hg19_hs_ideogr.RData", "class": [ "data.frame" ], "fields": [ "chrom", "chromStart", "chromEnd", "name", "gieStain" ], "rows": 862, "table": true, "tojson": true }, { "name": "LS041", "title": "Mapped reads in tumor and matched blood for patient LS041", "object": "LS041", "file": "LS041.RData", "class": [ "data.frame" ], "fields": [ "Chr", "Pos", "Test", "Norm", "GC" ], "rows": 7262, "table": true, "tojson": true } ], "_help": [ { "page": "addDNACopy-methods", "title": "Methods for Function addDNACopy in Package `CNAnorm'", "topics": [ "addDNACopy", "addDNACopy,CNAnorm-method", "addDNACopy-methods" ] }, { "page": "addSmooth-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "addSmooth", "addSmooth,CNAnorm-method", "addSmooth-methods" ] }, { "page": "chrsAndpos-methods", "title": "Accessors methods for Function ratio in Package `CNAnorm'", "topics": [ "arms", "arms,CNAnorm-method", "arms-methods", "chrs", "chrs-methods", "chrs<-", "chrs<--methods", "pos", "pos,CNAnorm-method", "pos-methods", "pos<-", "pos<--methods" ] }, { "page": "CN", "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.", "topics": [ "CN" ] }, { "page": "CNAnorm-class", "title": "Class \"CNAnorm\"", "topics": [ "chrs,CNAnorm-method", "chrs<-,CNAnorm-method", "CNAnorm", "CNAnorm-class", "length,CNAnorm-method", "pos<-,CNAnorm-method", "ratio,CNAnorm-method", "ratio.n,CNAnorm-method", "ratio.s,CNAnorm-method", "ratio.s.n,CNAnorm-method", "segMean,CNAnorm-method", "segMean.n,CNAnorm-method", "sugg.peaks,CNAnorm-method", "sugg.ploidy,CNAnorm-method", "valid.peaks,CNAnorm-method", "valid.ploidy,CNAnorm-method", "[,CNAnorm-method" ] }, { "page": "workflowWrapper", "title": "Wrapper to '\"CNAnorm\"' workflow", "topics": [ "CNAnormWorkflow" ] }, { "page": "dataFrame2object", "title": "Convert a data frame into an object of Class '\"CNAnorm\"'", "topics": [ "dataFrame2object" ] }, { "page": "DerivData-class", "title": "Class \"DerivData\"", "topics": [ "DerivData-class", "length,DerivData-method" ] }, { "page": "discreteNorm-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "discreteNorm", "discreteNorm,CNAnorm-method", "discreteNorm-methods" ] }, { "page": "exportTable-method", "title": "Methods for Function exportTable in Package `CNAnorm'", "topics": [ "exportTable", "exportTable,CNAnorm-method", "exportTable-methods" ] }, { "page": "gcNorm-methods", "title": "Methods for Function gcNorm in Package `CNAnorm'", "topics": [ "gcNorm", "gcNorm,CNAnorm-method", "gcNorm-methods" ] }, { "page": "gPar", "title": "An object with the default graphical parameters", "topics": [ "gPar" ] }, { "page": "data-hg19_hs_ideogr", "title": "An object with the ideogram information for homo sapiens - hg19", "topics": [ "hg19_hs_ideogr" ] }, { "page": "InData-class", "title": "Class \"InData\" ~~~", "topics": [ "InData-class", "length,InData-method" ] }, { "page": "LS041", "title": "Mapped reads in tumor and matched blood for patient LS041", "topics": [ "LS041" ] }, { "page": "Params-class", "title": "Class \"Params\"", "topics": [ "Params-class" ] }, { "page": "peakPloidy", "title": "Methods for Function peakPloidy in Package `CNAnorm'", "topics": [ "peakPloidy", "peakPloidy,CNAnorm-method", "peakPloidy-methods" ] }, { "page": "plotGenome-methods", "title": "Methods for Function plotGenome in Package `CNAnorm'", "topics": [ "plotGenome", "plotGenome,CNAnorm-method", "plotGenome-methods" ] }, { "page": "plotPeaks-methods", "title": "Methods for Function plotPeaks in Package `CNAnorm'", "topics": [ "plotPeaks", "plotPeaks,CNAnorm-method", "plotPeaks-methods" ] }, { "page": "ratio-methods", "title": "Methods for Function ratio in Package `CNAnorm'", "topics": [ "ratio", "ratio-methods", "ratio.n", "ratio.n-methods", "ratio.s", "ratio.s-methods", "ratio.s.n", "ratio.s.n-methods", "segMean", "segMean-methods", "segMean.n", "segMean.n-methods" ] }, { "page": "suggValid-methods", "title": "Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm'", "topics": [ "sugg.peaks", "sugg.peaks-methods", "sugg.ploidy", "sugg.ploidy-methods", "valid.peaks", "valid.peaks-methods", "valid.ploidy", "valid.ploidy-methods" ] }, { "page": "validation-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "validation", "validation,CNAnorm-method", "validation-methods" ] } ], "_rundeps": [ "DNAcopy" ], "_vignettes": [ { "source": "CNAnorm.Snw", "filename": "CNAnorm.pdf", "title": "An introduction to CNAnorm", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:19", "modified": "2014-03-05 16:55:42", "commits": 3 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "cnanorm", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T08:52:44.000Z", "distro": "noble", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "bbfdef9a43d5c7a48aefa9bc781d833c88ec2fddd74dda5f50d86451166acd47", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T08:53:40.000Z", "distro": "noble", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "8f6581ada8d3d80239fe982d794ef4e5f87afc5dafc4ff7607cd4dfd02c26048", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T08:53:14.000Z", "distro": "noble", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "6146bb4adcade4c87a96d77baf3c5b6c178a186efe3be9f0fe3b8889165d8170", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T08:53:25.000Z", "distro": "noble", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "30b25805da84e0fe389829ca9bcd7778f72077357c2fda38e4cc1763017536b4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-05-30T12:22:10.000Z", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "3d2fc78b36c618bac95158f5d2b8706e550b703d97832328c9f7f634921592a1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-05-30T08:54:01.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "96d86db5fa317ca16eb257f6cc957cc81d99485e2f3a99dd44105979aa640e11", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "mac", "version": "1.59.0", "date": "2026-05-30T12:22:18.000Z", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "72b5f1e90c5423a8be69c89fdd7054f8a8e0dd6d66988ebdf9ae43a5b7d61e5b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "mac", "version": "1.59.0", "date": "2026-05-30T08:55:53.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "7bb6308fa1bb3aaa4588a90648f52cbcd73549e455d91cffe22ff2ef56b37d98", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.0", "date": "2026-05-30T08:52:36.000Z", "arch": "emscripten", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "95d1b07feedec9eb8e5f095d6c8ef45374468c442afb7c850507eb75caec746f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-05-30T08:52:22.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "53fe8c2d9fe2a7dee70f8e46795a8a32fcf03f34f21d171815f6e1ee83dfabb3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-05-30T08:52:27.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "dc5130e78412e932dd0a9765486c1a937475ae7cbe2577ab49646979fed87a46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" }, { "r": "4.6.0", "os": "win", "version": "1.59.0", "date": "2026-05-30T08:51:57.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "12539b44bd4d18f4a72cc5b7f4d3b9fed02f3c6692db657d9f75f561e98419d4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679620292" } ] }