{ "_id": "6a34f2783efcd9bda43d09b6", "Package": "CNTools", "Version": "1.68.0", "Title": "Convert segment data into a region by sample matrix to allow for\nother high level computational analyses.", "Author": "Jianhua Zhang", "Maintainer": "J. Zhang ", "Description": "This package provides tools to convert the output of\nsegmentation analysis using DNAcopy to a matrix structure with\noverlapping segments as rows and samples as columns so that\nother computational analyses can be applied to segmented data", "Keyword": "copy number", "License": "LGPL", "ZipData": "no", "biocViews": "Microarray, CopyNumberVariation", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:33:57 UTC", "RemoteUrl": "https://github.com/bioc/CNTools", "RemoteRef": "RELEASE_3_23", "RemoteSha": "cd975ed20bf0c93e545334775fb103afbe27357e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-19 07:34:01 UTC", "User": "root" }, "MD5sum": "5e85ca1b278a829d676e71fee20e06a4", "_user": "bioc-release", "_type": "src", "_file": "CNTools_1.68.0.tar.gz", "_fileid": "45fb10fc88332de7bdc5b7e1a8227e566e9eaf76194cda4557a2c4b5233a54a6", "_filesize": 990483, "_sha256": "45fb10fc88332de7bdc5b7e1a8227e566e9eaf76194cda4557a2c4b5233a54a6", "_created": "2026-06-19T07:34:01.000Z", "_published": "2026-06-19T07:40:40.745Z", "_jobs": [ { "job": 82304945464, "time": 136, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7744194736" }, { "job": 82304945550, "time": 209, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7744215021" }, { "job": 82304945549, "time": 221, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7744217478" }, { "job": 82304945597, "time": 184, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7744208067" }, { "job": 82304945606, "time": 232, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7744220370" }, { "job": 82304945582, "time": 179, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7744206101" }, { "job": 82304945504, "time": 353, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7744252546" }, { "job": 82304945526, "time": 180, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7744206108" }, { "job": 82304945523, "time": 357, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7744253515" }, { "job": 82304512057, "time": 185, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7744156236" }, { "job": 82304945444, "time": 117, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7744189575" }, { "job": 82304945518, "time": 179, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7744206117" }, { "job": 82304945551, "time": 166, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7744202902" }, { "job": 82304945524, "time": 165, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7744202273" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CNTools", "_commit": { "id": "cd975ed20bf0c93e545334775fb103afbe27357e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379637 }, "_maintainer": { "name": "J. Zhang", "email": "jzhang@jimmy.harvard.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "tools", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "genefilter", "role": "Depends" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.69.0", "bioc": "3.24" }, { "branch": "release", "version": "1.68.0", "bioc": "3.23" } ], "_topics": [ "microarray", "copynumbervariation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 21, "_searchresults": 44, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNTools.html", "extra/contents.json", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "CNSeg", "diffBy", "genefilter", "getCor", "getDist", "getRS", "madFilter", "rs", "rs<-", "segBy", "segList", "segList<-", "show" ], "_datasets": [ { "name": "geneInfo", "title": "method that convert segment data into reduced segment matrix", "object": "geneInfo", "file": "geneInfo.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "geneid", "genename" ], "rows": 28918, "table": true, "tojson": true }, { "name": "sampleData", "title": "Class \"CNSeg\" contains the output of DNACopy segmentation data that can be operated on by the associated methods", "object": "sampleData", "file": "sampleData.rda", "class": [ "data.frame" ], "fields": [ "ID", "chrom", "loc.start", "loc.end", "num.mark", "seg.mean" ], "rows": 54825, "table": true, "tojson": true } ], "_help": [ { "page": "CNSeg-class", "title": "Class \"CNSeg\" contains the output of DNACopy segmentation data that can be operated on by the associated methods", "topics": [ "CNSeg", "CNSeg-class", "sampleData", "segList", "segList,CNSeg-method", "segList-method", "segList<-", "segList<-,CNSeg-method", "show,CNSeg-method" ] }, { "page": "diffBy-methods", "title": "A filter that filters out features that do not differ by a set threshold between a pair of samples", "topics": [ "diffBy", "diffBy,ANY-method", "diffBy,RS-method", "diffBy-method" ] }, { "page": "dist-methods", "title": "A method that extends the generic function dist to handle reduced segemnts", "topics": [ "getDist", "getDist,ANY-method", "getDist,RS-method", "getDist-method" ] }, { "page": "genefilter-methods", "title": "A method that filters feature based on reduced segment", "topics": [ "genefilter,RS-method", "genefilter-methods" ] }, { "page": "cor-methods", "title": "Method that extends the cor function of stats to handle reduced segment data", "topics": [ "getCor", "getCor,ANY-method", "getCor,RS-method", "getCor-method" ] }, { "page": "getRS-methods", "title": "method that convert segment data into reduced segment matrix", "topics": [ "geneInfo", "getRS", "getRS,CNSeg-method", "getRS-method" ] }, { "page": "madFilter-methods", "title": "Method that filters reduced segment matrix by the mean absolute deviation", "topics": [ "madFilter", "madFilter,ANY-method", "madFilter,RS-method", "madFilter-method" ] }, { "page": "RS-class", "title": "Class \"RS\" contains the Reduced Segment data matrix derived from the output of segmentation", "topics": [ "rs", "rs,RS-method", "RS-class", "rs<-", "rs<-,RS-method", "segBy", "segBy,RS-method", "show,RS-method" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "genefilter", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "HowTo.Rnw", "filename": "HowTo.pdf", "title": "NCTools HowTo", "engine": "utils::Sweave", "headings": [ "Session Infor" ], "created": "2013-11-01 20:08:49", "modified": "2013-11-01 20:08:49", "commits": 1 } ], "_score": 5.421603926869831, "_indexed": false, "_nocasepkg": "cntools", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/CNTools", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.68.0", "date": "2026-06-19T07:36:44.000Z", "distro": "noble", "arch": "aarch64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "0b0a51c6396fafe747ec2744b1d2b435ae5c8fb625bdd2fa4a2df6234c1e8d92", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.7.0", "os": "linux", "version": "1.68.0", "date": "2026-06-19T07:36:29.000Z", "distro": "noble", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "12114671d31d37f8389892cb3420949f59c8f098d081cef9ce53b9e1d5f81594", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "linux", "version": "1.68.0", "date": "2026-06-19T07:36:18.000Z", "distro": "noble", "arch": "aarch64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "84b3ac90659ca25835954bc169adfe4a3394fad0b65252a94374da840e7ed284", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "linux", "version": "1.68.0", "date": "2026-06-19T07:36:43.000Z", "distro": "noble", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "da47ecc65727f3304dd10754dfbc373fb4c197c907bba337523a3ac7f03124be", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.5.3", "os": "mac", "version": "1.68.0", "date": "2026-06-19T07:36:03.000Z", "arch": "aarch64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "a0100477240c462cb77194a2ef4fa87005f2e4172bcc3205d500a47e655bb484", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.5.3", "os": "mac", "version": "1.68.0", "date": "2026-06-19T07:37:31.000Z", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "799034e499ff781e46e176532329cb22e0a1aa0749c3348c40623c0b7e26187b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "mac", "version": "1.68.0", "date": "2026-06-19T07:35:51.000Z", "arch": "aarch64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "2dc692d546f73ba47a8acaf52f442c574c8f8bb007b7c989e112855824df76e2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "mac", "version": "1.68.0", "date": "2026-06-19T07:37:50.000Z", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "5e43efb7f4ab79ce5f9bafd1076a04c2c35be8ce09e56dfc42d0a040c4e6af7e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "wasm", "version": "1.68.0", "date": "2026-06-19T07:36:20.000Z", "arch": "emscripten", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "89ad2b9ccef3458ab64afcbef29c9cdc8c95d800a3163843f7f9255e067fca48", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.7.0", "os": "win", "version": "1.68.0", "date": "2026-06-19T07:35:34.000Z", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "26f1c6f60ab98796a89880a0ecefacbbf621a8a996f4343b0152841aa69685a0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.5.3", "os": "win", "version": "1.68.0", "date": "2026-06-19T07:35:32.000Z", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "d468931f456576cd81507d36335d43ec2da4df53d101da7779ca1b8f55c44ebb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" }, { "r": "4.6.0", "os": "win", "version": "1.68.0", "date": "2026-06-19T07:35:33.000Z", "arch": "x86_64", "commit": "cd975ed20bf0c93e545334775fb103afbe27357e", "fileid": "5e671937259223e71ff26de8783b3e4a64790605766e4bd5f81aa1cd78701040", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27812054111" } ] }