{ "_id": "6a4790008b9f0d9747cf13d1", "Package": "jointseg", "Type": "Package", "Title": "Joint Segmentation of Multivariate (Copy Number) Signals", "Version": "1.0.2", "Authors@R": "c(person(\"Morgane\", \"Pierre-Jean\", role = c(\"aut\", \"cre\"), \nemail = \"mpierrejean.pro@gmail.com\"),\nperson(\"Pierre\", \"Neuvial\", role = c(\"aut\"),\nemail=\"pierre.neuvial@math.univ-toulouse.fr\"),\nperson(\"Guillem\", \"Rigaill\", role = \"aut\"))", "Description": "Methods for fast segmentation of multivariate signals into\npiecewise constant profiles and for generating realistic\ncopy-number profiles. A typical application is the joint\nsegmentation of total DNA copy numbers and allelic ratios\nobtained from Single Nucleotide Polymorphism (SNP) microarrays\nin cancer studies. The methods are described in Pierre-Jean,\nRigaill and Neuvial (2015) .", "License": "LGPL (>= 2.1)", "VignetteBuilder": "knitr", "URL": "https://github.com/mpierrejean/jointseg", "RoxygenNote": "6.1.1", "BugReports": "https://github.com/mpierrejean/jointseg/issues", "Repository": "https://mpierrejean.r-universe.dev", "Date/Publication": "2019-01-07 10:58:45 UTC", "RemoteUrl": "https://github.com/mpierrejean/jointseg", "RemoteRef": "HEAD", "RemoteSha": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-02 08:35:28 UTC", "User": "root" }, "Author": "Morgane Pierre-Jean [aut, cre],\nPierre Neuvial [aut],\nGuillem Rigaill [aut]", "Maintainer": "Morgane Pierre-Jean ", "_user": "mpierrejean", "_type": "src", "_file": "jointseg_1.0.2.tar.gz", "_fileid": "https://r2.ropensci.org/3c057f1f9de456cf51cafba11305f792c834a6ca9ef7af967d5fd5b1909feed1", "_filesize": 2944852, "_sha256": "3c057f1f9de456cf51cafba11305f792c834a6ca9ef7af967d5fd5b1909feed1", "_expires": "2026-10-11T10:33:35.000Z", "_created": "2026-07-02T08:35:28.000Z", "_published": "2026-07-03T10:33:36.726Z", "_jobs": [ { "job": 84981526204, "time": 150, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8033306852" }, { "job": 84981525852, "time": 137, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8033301481" }, { "job": 84981525934, "time": 151, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8033307506" }, { "job": 84981526159, "time": 144, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8033304317" }, { "job": 84981525946, "time": 185, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8033304861" }, { "job": 84981525973, "time": 245, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8033334066" }, { "job": 84981525823, "time": 138, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8033293791" }, { "job": 84981525777, "time": 302, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8033352779" }, { "job": 84981525584, "time": 183, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8033249909" }, { "job": 84981525969, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8033294562" }, { "job": 84981526131, "time": 106, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8033291184" }, { "job": 84981525917, "time": 96, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8033287620" }, { "job": 84981526279, "time": 209, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8033327897" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774", "_status": "success", "_upstream": "https://github.com/mpierrejean/jointseg", "_commit": { "id": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "author": "Morgane Pierre-Jean ", "committer": "GitHub ", "message": "Merge pull request #11 from mpierrejean/develop\n\nDevelop", "time": 1546858725 }, "_maintainer": { "name": "Morgane Pierre-Jean", "email": "mpierrejean.pro@gmail.com", "login": "mpierrejean", "description": "", "uuid": 11524264 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "acnr", "version": ">= 0.3.1", "role": "Imports" }, { "package": "matrixStats", "version": ">= 0.6.0", "role": "Imports" }, { "package": "DNAcopy", "role": "Imports" }, { "package": "PSCBS", "role": "Suggests" }, { "package": "R.cache", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "changepoint", "version": ">= 1.0.2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "mpierrejean", "_selfowned": true, "_usedby": 2, "_updates": [], "_tags": [], "_stars": 7, "_contributors": [ { "user": "pneuvial", "count": 72, "uuid": 7895899 }, { "user": "mpierrejean", "count": 6, "uuid": 11524264 }, { "user": "guillemr", "count": 5, "uuid": 10654267 } ], "_userbio": { "uuid": 11524264, "type": "user", "name": "Morgane Pierre-Jean", "followers": 3 }, "_downloads": { "count": 357, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/jointseg" }, "_devurl": "https://github.com/mpierrejean/jointseg", "_searchresults": 61, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/jointseg.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mpierrejean/jointseg", "_realowner": "mpierrejean", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2017-11-27" }, { "version": "1.0.1", "date": "2017-11-28" }, { "version": "1.0.2", "date": "2019-01-11" }, { "version": "1.0.3", "date": "2025-05-14" } ], "_exports": [ "anotherBkp", "binMissingValues", "defaultWeights", "doCBS", "doDynamicProgramming", "doGFLars", "doPSCBS", "doPSCN", "doRBS", "estimateSd", "Fpsn", "getCopyNumberDataByResampling", "getTpFp", "jointSeg", "leftMultiplyByInvXAtXA", "leftMultiplyByXt", "modelSelection", "multiplyXtXBySparse", "oneBkp", "plotSeg", "pruneByDP", "PSSeg", "randomProfile", "segmentByGFLars", "segmentByRBS" ], "_help": [ { "page": "binMissingValues", "title": "binMissingValues", "topics": [ "binMissingValues" ] }, { "page": "doCBS", "title": "Run CBS segmentation", "topics": [ "doCBS" ] }, { "page": "doDynamicProgramming", "title": "Run segmentation by dynamic programming", "topics": [ "doDynamicProgramming" ] }, { "page": "doGFLars", "title": "Group fused Lars segmentation", "topics": [ "doGFLars" ] }, { "page": "doPSCBS", "title": "Run Paired PSCBS segmentation", "topics": [ "doPSCBS" ] }, { "page": "doPSCN", "title": "Run PSCN segmentation (defunct)", "topics": [ "doPSCN" ] }, { "page": "doRBS", "title": "Run RBS segmentation", "topics": [ "doRBS" ] }, { "page": "estimateSd", "title": "Robust standard deviation estimator", "topics": [ "estimateSd" ] }, { "page": "Fpsn", "title": "Pruned dynamic programming algorithm", "topics": [ "Fpsn" ] }, { "page": "getCopyNumberDataByResampling", "title": "Generate a copy number profile by resampling", "topics": [ "getCopyNumberDataByResampling" ] }, { "page": "getTpFp", "title": "Calculate the number of true positives and false positives", "topics": [ "getTpFp" ] }, { "page": "jointSeg", "title": "Joint segmentation of multivariate signals", "topics": [ "jointSeg" ] }, { "page": "mapPositionsBack", "title": "mapPositionsBack", "topics": [ "mapPositionsBack" ] }, { "page": "modelSelection", "title": "Model selection", "topics": [ "modelSelection" ] }, { "page": "plotSeg", "title": "Plot signal and breakpoints with segment-level signal estimates", "topics": [ "plotSeg" ] }, { "page": "pruneByDP", "title": "Exact segmentation of a multivariate signal using dynamic programming.", "topics": [ "pruneByDP" ] }, { "page": "PSSeg", "title": "Parent-Specific copy number segmentation", "topics": [ "PSSeg" ] }, { "page": "randomProfile", "title": "Generate a random multi-dimensional profile with breakpoints and noise", "topics": [ "randomProfile" ] }, { "page": "retour_sn", "title": "Extract endpoint matrix from DP result", "topics": [ "retour_sn" ] }, { "page": "segmentByGFLars", "title": "Group fused Lars segmentation (low-level)", "topics": [ "segmentByGFLars" ] }, { "page": "segmentByRBS", "title": "Recursive Binary Segmentation (low-level)", "topics": [ "segmentByRBS" ] } ], "_readme": "https://github.com/mpierrejean/jointseg/raw/HEAD/README.md", "_rundeps": [ "acnr", "DNAcopy", "matrixStats" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "dataGeneration.Rmd", "filename": "dataGeneration.html", "title": "Generating realistic data with known truth using the jointseg package", "author": "M. Pierre-Jean, G. Rigaill, P. Neuvial", "engine": "knitr::rmarkdown", "headings": [ "Citing jointseg", "Setup", "Affymetrix data", "Illumina data", "Session information", "References" ], "created": "2016-12-16 09:13:34", "modified": "2019-01-07 10:34:36", "commits": 4 }, { "source": "PSSeg.Rmd", "filename": "PSSeg.html", "title": "PSSeg: Parent-Specifc copy number segmentation", "author": "M. Pierre-Jean, G. Rigaill, P. Neuvial", "engine": "knitr::rmarkdown", "headings": [ "Preparing data to be segmented", "Preprocessing", "PSSeg segmentation using RBS", "Initial segmentation and pruning", "Plot segmented profile", "Results evaluation", "Session information", "Citing jointseg", "References" ], "created": "2016-12-15 23:56:11", "modified": "2017-11-30 07:39:53", "commits": 3 } ], "_score": 6.709609121072649, "_indexed": true, "_nocasepkg": "jointseg", "_universes": [ "mpierrejean" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-07-02T08:37:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/24598298eca8cd3963b33fdff3ca5c97f3b0ed090fa02f1cc94ca1fe07230c14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-07-02T08:37:37.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/a0f9af45633633aa4f7defdd7499f4f22b143abae5982386658b5fdafb39306e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-07-02T08:37:59.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/f9631b5dc56928add913150691c6c099b8b29ed2afaf24af68ccf85acf432016", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-07-02T08:37:43.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/baddb4a254a15ff495ffc3a85bfd878ec14a7b896c7de7c114976b89a170e357", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-07-02T08:37:46.000Z", "arch": "aarch64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/47c6ac00e7cb7edea01eee467fc27061d49d7032b639c40649e67cec64e007fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-07-02T08:38:43.000Z", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/d78f50e390528b282792ccbc10047eabdefd7bbe75dfee554e8be63c2cfe6b5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-07-02T08:37:17.000Z", "arch": "aarch64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/a8cce680aae7ade98c4c5787a3295fd214724d782bb873f95b76885f075bc4c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-07-02T08:39:26.000Z", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/f5b4edca190485f8857fc1336b867256a5c71620b6a8625c905dd2eabdab1bfd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-07-02T08:37:42.000Z", "arch": "emscripten", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/c28b3dcfd8ce6d8b7ca6647da114e4614659e08f6592a3a193fe50dd050990b3", "status": "success", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-07-02T08:36:49.000Z", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/066e4f06aa1087a6828bbfd106d71662b0f704171d4f7980ede5abfc548fb7d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-07-02T08:36:42.000Z", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/af92a5d925fa00cfc2e20d0e3c9723240a9d538dc305b0b14dddc91399653c9e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" }, { "r": "4.6.1", "os": "win", "version": "1.0.2", "date": "2026-07-02T08:38:22.000Z", "arch": "x86_64", "commit": "5b7ab68d331dc0311264b28ceb264e35d96fb0a2", "fileid": "https://r2.ropensci.org/442f10924c26530abf5dfc72ea9f6cb6ed9cbbe17ec9f82e11c12c1b98f0bb87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mpierrejean/actions/runs/28576573774" } ] }