{ "_id": "6a214072cd65a98ecbd2a3d0", "Package": "ctl", "Version": "1.0.0-10", "Date": "2024-01-15", "Title": "Correlated Trait Locus Mapping", "Author": "Danny Arends , Yang Li, Gudrun A\nBrockmann, Ritsert C Jansen, Robert W Williams, and Pjotr Prins", "Maintainer": "Danny Arends ", "Description": "Identification and network inference of genetic loci\nassociated with correlation changes in quantitative traits\n(called correlated trait loci, CTLs). Arends et al. (2016)\n.", "Encoding": "UTF-8", "ByteCompile": "true", "License": "GPL-3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-04 08:59:03 UTC", "User": "root" }, "Repository": "https://dannyarends.r-universe.dev", "Date/Publication": "2024-01-17 02:40:37 UTC", "RemoteUrl": "https://github.com/cran/ctl", "RemoteRef": "HEAD", "RemoteSha": "51422439e805d6231995e70fb35ec6a15e03c426", "MD5sum": "e52986e0ca65821bbaa0843d9f61e676", "_user": "dannyarends", "_type": "src", "_file": "ctl_1.0.0-10.tar.gz", "_fileid": "acb9cf8ef961b755c3d92ce2b4ec27acf63398e405be18ccb508b9ddf75f0402", "_filesize": 4005552, "_sha256": "acb9cf8ef961b755c3d92ce2b4ec27acf63398e405be18ccb508b9ddf75f0402", "_created": "2026-06-04T08:59:03.000Z", "_published": "2026-06-04T09:08:02.731Z", "_distro": "noble", "_jobs": [ { "job": 79484880886, "time": 130, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7407323523" }, { "job": 79484880958, "time": 115, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7407317806" }, { "job": 79484880962, "time": 139, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7407326859" }, { "job": 79484880877, "time": 106, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7407314532" }, { "job": 79484880892, "time": 192, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7407332905" }, { "job": 79484880907, "time": 488, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7407427880" }, { "job": 79484880893, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7407316928" }, { "job": 79484880890, "time": 249, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7407356055" }, { "job": 79484449850, "time": 157, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7407279873" }, { "job": 79484880832, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7407311789" }, { "job": 79484881018, "time": 119, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7407318642" }, { "job": 79484880891, "time": 84, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7407307413" }, { "job": 79484880978, "time": 128, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7407321905" } ], "_buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/ctl", "_commit": { "id": "51422439e805d6231995e70fb35ec6a15e03c426", "author": "Danny Arends ", "committer": "cran-robot ", "message": "version 1.0.0-10\n", "time": 1705459237 }, "_maintainer": { "name": "Danny Arends", "email": "danny.arends@gmail.com", "login": "dannyarends", "orcid": "0000-0001-8738-0162", "twitter": "@DannyArends", "description": "World-class geneticist, Lecturencer, ESPRIT Fanboy, and Associate Professor in Bioinformatics at Northumbria University.", "uuid": 47902 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "parallel", "role": "Depends" }, { "package": "qtl", "role": "Depends" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "dannyarends", "count": 8, "uuid": 47902 } ], "_userbio": { "uuid": 47902, "type": "user", "name": "Danny Arends", "description": "World-class geneticist, Lecturencer, ESPRIT Fanboy, and Associate Professor in Bioinformatics at Northumbria University." }, "_downloads": { "count": 197, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ctl" }, "_mentions": 2, "_searchresults": 102, "_topics": [ "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ctl.html", "manual.pdf" ], "_realowner": "dannyarends", "_cranurl": false, "_releases": [ { "version": "1.0.0-0", "date": "2016-09-20" }, { "version": "1.0.0-1", "date": "2018-07-06" }, { "version": "1.0.0-2", "date": "2018-08-03" }, { "version": "1.0.0-4", "date": "2019-12-16" }, { "version": "1.0.0-7", "date": "2022-02-09" }, { "version": "1.0.0-8", "date": "2023-01-16" }, { "version": "1.0.0-9", "date": "2023-11-27" }, { "version": "1.0.0-10", "date": "2024-01-16" } ], "_exports": [ "a_loc", "addChromosomeLines", "basic.qc", "check.genotypes", "check.marker", "check.pheno", "chiSQN", "chiSQtoP", "chr_length", "chr_total_length", "circle.loc", "correlated.phenotype", "correlation", "create.marker", "ctl.circle", "ctl.ctlmatrix", "ctl.dcormatrix", "ctl.lineplot", "ctl.load", "ctl.name", "ctl.names", "ctl.qtlmatrix", "ctl.qtlprofile", "ctl.version", "CTLanalyseEffects", "CTLanalyseRatios", "CTLasLOD", "ctleffects", "CTLmapping", "ctlmarker", "CTLnetwork", "CTLnetwork.addmarker", "CTLpowerAnalysis", "CTLprofiles", "CTLregions", "CTLscan", "CTLscan.cross", "CTLscantoScanone", "CTLsignificant", "CTLtoLODvector", "dcor", "dcor.create", "deltaSD", "detect.peaks", "draw.element", "draw.spline", "gcLoop", "get.chr.edges", "getCorrelations", "getCorrelations.cross", "getPermuteThresholds", "getRatio", "getRVM", "hist.CTLobject", "image.CTLobject", "internal.image", "lodscorestoscanone", "m_loc", "mapinfotomarkerlocs", "munique", "nfrom", "nto", "openmp", "plot.CTLnetwork", "plot.CTLobject", "plot.CTLpermute", "plot.CTLscan", "plotCTLscan3", "plotExpression", "plotTraits", "print.CTLobject", "print.CTLpermute", "print.CTLscan", "printSignificantSlope", "qtlimage", "QTLmapping", "redblue", "remove.diag", "scanSD", "scanSD.cross", "scanSlopes", "scanSlopes.cross", "stdSlopeBeta", "stdSlopeError", "stdSlopeEstimate", "stdSlopeIntercept", "stdSlopeTest", "test.chiSQN", "test.correlation", "test.getCorrelation.cross", "test.power.test", "top.correlated", "whiteblack" ], "_datasets": [ { "name": "ath.churchill", "title": "Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.", "object": "ath.churchill", "file": "ath.churchill.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ath.gary", "title": "Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.", "object": "ath.churchill", "file": "ath.churchill.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ath.metab", "title": "Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.", "object": "ath.metabolites", "file": "ath.metabolites.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ath.metabolites", "title": "Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.", "object": "ath.metabolites", "file": "ath.metabolites.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ath.result", "title": "Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.", "object": "ath.result", "file": "ath.result.RData", "class": [ "list", "CTLobject" ], "fields": [], "table": true, "tojson": true }, { "name": "yeast.brem", "title": "Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.", "object": "yeast.brem", "file": "yeast.brem.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "ctl-package", "title": "CTL - CTL mapping in experimental crosses", "topics": [ "CTL", "ctl" ] }, { "page": "ath.churchill", "title": "Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.", "topics": [ "ath.churchill", "ath.gary" ] }, { "page": "ath.metabolites", "title": "Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.", "topics": [ "ath.metab", "ath.metabolites" ] }, { "page": "ath.result", "title": "Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.", "topics": [ "ath.result" ] }, { "page": "basic.qc", "title": "Create quality control plots.", "topics": [ "basic.qc" ] }, { "page": "ctl.circle", "title": "Circleplot CTL on multiple traits", "topics": [ "ctl.circle" ] }, { "page": "ctl.lineplot", "title": "Lineplot CTL on multiple traits", "topics": [ "ctl.lineplot" ] }, { "page": "ctl.load", "title": "ctl.load - Load CTLs calculated by the D2.0 version", "topics": [ "ctl.load" ] }, { "page": "ctl.helper", "title": "CTLhelper - Helper functions for CTL mapping", "topics": [ "ctl.ctlmatrix", "ctl.dcormatrix", "ctl.name", "ctl.names", "ctl.qtlmatrix", "ctl.qtlprofile" ] }, { "page": "ctl.mapping", "title": "CTLmapping - Scan for correlated trait loci (CTL)", "topics": [ "CTLmapping" ] }, { "page": "ctl.network", "title": "CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits", "topics": [ "CTLnetwork" ] }, { "page": "ctl.profiles", "title": "CTLprofiles - Extract CTL interaction profiles", "topics": [ "CTLprofiles" ] }, { "page": "ctl.regions", "title": "CTLregions - Get all significant interactions from a genome-wide CTLscan", "topics": [ "CTLregions" ] }, { "page": "ctl.scan", "title": "CTLscan - Scan for Correlated Trait Locus (CTL)", "topics": [ "CTLscan" ] }, { "page": "ctl.scan.cross", "title": "CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object)", "topics": [ "CTLscan.cross" ] }, { "page": "ctl.significant", "title": "CTLsignificant - Get all significant interactions from a genome-wide CTLscan", "topics": [ "CTLsignificant" ] }, { "page": "detect.peaks", "title": "detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold", "topics": [ "detect.peaks" ] }, { "page": "ctl.hist", "title": "Plot histogram of CTL permutations", "topics": [ "hist.CTLobject" ] }, { "page": "ctl.image", "title": "Plot genome-wide CTL on multiple traits", "topics": [ "image.CTLobject" ] }, { "page": "ctl.plot.ctlobject", "title": "Plot CTL curves or heatmaps", "topics": [ "plot.CTLobject" ] }, { "page": "ctl.permute.plot", "title": "Differential correlation versus likelihood plotted in curves", "topics": [ "plot.CTLpermute" ] }, { "page": "ctl.plot.ctlscan", "title": "Plot CTL results as bar, line or GWAS plot.", "topics": [ "plot.CTLscan" ] }, { "page": "plotTraits", "title": "plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus", "topics": [ "plotTraits" ] }, { "page": "ctl.print.ctlobject", "title": "Print the results of a CTL genome scan", "topics": [ "print.CTLobject" ] }, { "page": "ctl.print.ctlscan", "title": "Print the results of a single phenotype CTL scan", "topics": [ "print.CTLscan" ] }, { "page": "qtl.image", "title": "Plot a QTL heatmap of the phenotypes scanned by CTLscan", "topics": [ "qtlimage" ] }, { "page": "qtl.mapping", "title": "QTLmapping - QTL mapping method for CTL analysis", "topics": [ "QTLmapping" ] }, { "page": "scanSD", "title": "scanSD - Analyze the differences in Standard Deviation between genotypes between two traits", "topics": [ "scanSD" ] }, { "page": "scanSD.cross", "title": "scanSD.cross - Analyze the differences in standard deviation between two traits at a certain genetic marker (R/qtl cross object)", "topics": [ "scanSD.cross" ] }, { "page": "scanSlopes", "title": "scanSlopes - Create a slope difference profile between two traits", "topics": [ "scanSlopes" ] }, { "page": "scanSlopes.cross", "title": "scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)", "topics": [ "scanSlopes.cross" ] }, { "page": "yeast.brem", "title": "Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.", "topics": [ "yeast.brem" ] } ], "_rundeps": [ "MASS", "qtl" ], "_sysdeps": [ { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "manual.Rnw", "filename": "manual.pdf", "title": "Manual", "engine": "utils::Sweave", "headings": [], "created": "2016-09-20 15:39:01", "modified": "2023-11-28 02:39:39", "commits": 4 } ], "_score": 3.3096301674258988, "_indexed": true, "_nocasepkg": "ctl", "_universes": [ "dannyarends" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0-10", "date": "2026-06-04T09:01:12.000Z", "distro": "noble", "arch": "aarch64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "9b50523e5345d038e60cf1ef4c6b58d570e99f4674e7bae6b10b615ea3b5f7aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0-10", "date": "2026-06-04T09:00:52.000Z", "distro": "noble", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "9e3639827074db7735d74a754f88b894336e0f3f5895c0d512aaee66924794ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0-10", "date": "2026-06-04T09:01:23.000Z", "distro": "noble", "arch": "aarch64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "0e821a2d743a7ec42e35920156820f9b39105ddb06571a87bbc0cadd21d32f6c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0-10", "date": "2026-06-04T09:00:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "4ee1a5736a7b1ed3dbab3706a22fb7214aa845da5042c06651c6f4986e29bc3d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0-10", "date": "2026-06-04T09:01:36.000Z", "arch": "aarch64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "b9d188d92bd6f4ea4763f2a716c2289b9b237ffa7a07c0441e2af0638cfe2dfe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0-10", "date": "2026-06-04T09:05:29.000Z", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "a71dec84f07f8d6974b11be901c989cac165ec004e2299e7966250db044e1a66", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0-10", "date": "2026-06-04T09:00:55.000Z", "arch": "aarch64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "75aa2ab03f3f5aa829815ed5dac7553b401c60ffe980ad16d20ee4509079dd79", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0-10", "date": "2026-06-04T09:02:20.000Z", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "07a2331116248ce5a04654787915c0f63aea593e0d1b4510aae228102e4ddd23", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0-10", "date": "2026-06-04T09:00:59.000Z", "arch": "emscripten", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "091894ddab3a66d3be2eaa59fc1c7aed6b8c086dc5679144b8de6f291a29c5de", "status": "success", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.7.0", "os": "win", "version": "1.0.0-10", "date": "2026-06-04T09:00:34.000Z", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "3aa09e37eb45fc1068fbc8cb1d21c269ac24ced078832e2422617cb8dc13c205", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.5.3", "os": "win", "version": "1.0.0-10", "date": "2026-06-04T09:00:08.000Z", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "76f85425f3e7b26bd75a39133fa2f54958681444d5d763d42ed119fcf947256a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" }, { "r": "4.6.0", "os": "win", "version": "1.0.0-10", "date": "2026-06-04T09:00:36.000Z", "arch": "x86_64", "commit": "51422439e805d6231995e70fb35ec6a15e03c426", "fileid": "7cf2ecc0d4a593ea10163d84cae83ba2ad630ce9f074e86789189cc67d9aa58f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dannyarends/actions/runs/26941640910" } ] }