{ "_id": "6a129d1eacfb0bcc41d0f2ff", "Package": "GLAD", "Version": "2.76.0", "Date": "2020-04-15", "Title": "Gain and Loss Analysis of DNA", "SystemRequirements": "gsl. Note: users should have GSL installed. Windows\nusers: 'consult the README file available in the inst directory\nof the source distribution for necessary configuration\ninstructions'.", "Author": "Philippe Hupe", "Maintainer": "Philippe Hupe ", "Description": "Analysis of array CGH data : detection of breakpoints in\ngenomic profiles and assignment of a status (gain, normal or\nloss) to each chromosomal regions identified.", "License": "GPL-2", "URL": "http://bioinfo.curie.fr", "biocViews": "Microarray, CopyNumberVariation", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "libgsl0-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:30:46 UTC", "RemoteUrl": "https://github.com/bioc/GLAD", "RemoteRef": "RELEASE_3_23", "RemoteSha": "36043955d9a38510ccce25e6da64498c9d83dfe5", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-24 06:35:33 UTC", "User": "root" }, "MD5sum": "81e59caeedba73c9b6e11a07915a6354", "_user": "bioc-release", "_type": "src", "_file": "GLAD_2.76.0.tar.gz", "_fileid": "f1db0c02b572ed234ea438afe00d95f06429762a72a666c78e2a736534002bfd", "_filesize": 1454047, "_sha256": "f1db0c02b572ed234ea438afe00d95f06429762a72a666c78e2a736534002bfd", "_created": "2026-05-24T06:35:33.000Z", "_published": "2026-05-24T06:39:26.653Z", "_jobs": [ { "job": 77577700656, "time": 148, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7182935506" }, { "job": 77577700667, "time": 136, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7182934291" }, { "job": 77577700676, "time": 164, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7182936961" }, { "job": 77577700688, "time": 149, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7182935669" }, { "job": 77577700681, "time": 153, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7182935858" }, { "job": 77577700685, "time": 95, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7182930454" }, { "job": 77577700683, "time": 191, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7182939693" }, { "job": 77577700679, "time": 82, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7182929303" }, { "job": 77577700687, "time": 194, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7182939906" }, { "job": 77577514459, "time": 230, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7182921477" }, { "job": 77577700621, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7182932165" }, { "job": 77577700622, "time": 125, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7182933358" }, { "job": 77577700626, "time": 99, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7182930761" }, { "job": 77577700631, "time": 130, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7182933748" } ], "_bioccheck": { "error": 3, "warning": 6, "note": 18 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GLAD", "_commit": { "id": "36043955d9a38510ccce25e6da64498c9d83dfe5", "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": 1777379446 }, "_maintainer": { "name": "Philippe Hupe", "email": "glad@curie.fr" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "aws", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.77.0", "bioc": "3.24" }, { "branch": "release", "version": "2.76.0", "bioc": "3.23" } ], "_topics": [ "microarray", "copynumbervariation", "gsl", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 726, "source": "https://www.bioconductor.org/packages/stats/bioc/GLAD" }, "_mentions": 81, "_searchresults": 124, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GLAD.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "affectationGNL", "affectationGNL.profileCGH", "arrayPersp", "arrayPersp.arrayCGH", "arrayPersp.default", "arrayPlot", "arrayPlot.arrayCGH", "arrayPlot.default", "as.data.frame.profileCGH", "as.profileCGH", "as.profileCGH.data.frame", "BkpInfo", "BkpInfo.profileCGH", "CheckData", "CheckData.profileCGH", "chrBreakpoints", "chrBreakpoints.profileCGH", "ChrNumeric", "clusterglad", "clusterglad.hclust", "ColorBar", "daglad", "daglad.profileCGH", "DelRegionTooSmall", "detectOutliers", "detectOutliers.profileChr", "dogenomestep", "FDRThres", "filterBkp", "filterBkp.profileCGH", "filterBkpStep", "filterBkpStep.profileCGH", "findCluster", "findCluster.profileChr", "glad", "glad.profileCGH", "HaarSeg", "HaarSegGLAD", "HaarSegGLADCPP", "hclustglad", "kernelpen", "lawsglad", "loopRemove", "loopRemove.profileChr", "MoveBkp", "MoveBkp.profileCGH", "MoveBkpStep", "MoveBkpStep.profileCGH", "myPalette", "OptimBkpFindCluster", "OutliersGNL", "OutliersGNL.profileCGH", "plotCytoBand", "plotCytoBand.default", "plotProfile", "plotProfile.profileCGH", "prepare.output.daglad", "RecomputeGNL", "removeBreakpoints", "removeBreakpoints.profileChr", "removeLevel", "removeLevel.profileChr", "SegmentByPeaks", "selectindex", "testBkpToMove", "testBkpToMove.profileCGH" ], "_datasets": [ { "name": "array1", "title": "Bladder cancer CGH data", "object": "arrayCGH", "file": "arrayCGH.RData", "class": [ "data.frame" ], "fields": [ "Log2Rat", "Row", "Col", "Position", "CHROMOSOME" ], "rows": 7392, "table": true, "tojson": true }, { "name": "array2", "title": "Bladder cancer CGH data", "object": "arrayCGH", "file": "arrayCGH.RData", "class": [ "data.frame" ], "fields": [ "Log2Rat", "Row", "Col", "Position", "CHROMOSOME" ], "rows": 7392, "table": true, "tojson": true }, { "name": "array3", "title": "Bladder cancer CGH data", "object": "arrayCGH", "file": "arrayCGH.RData", "class": [ "data.frame" ], "fields": [ "Log2Rat", "Row", "Col", "Position", "CHROMOSOME" ], "rows": 7392, "table": true, "tojson": true }, { "name": "cytoband", "title": "Cytogenetic banding", "object": "cytoband", "file": "cytoband.RData", "class": [ "data.frame" ], "fields": [ "Chromosome", "Band", "Start", "End", "Centro", "Color", "ChrNumeric" ], "rows": 395, "table": true, "tojson": true }, { "name": "gm00143", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm01524", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm01535", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm01750", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm02948", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm03134", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm03563", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm03576", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm04435", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm05296", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm07081", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm07408", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm10315", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm13031", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "gm13330", "title": "Public CGH data of Snijders", "object": "snijders", "file": "snijders.RData", "class": [ "data.frame" ], "fields": [ "PosOrder", "LogRatio", "PosBase", "Chromosome", "BAC", "Statut" ], "rows": 2271, "table": true, "tojson": true }, { "name": "P20", "title": "Public CGH data of Veltman", "object": "veltman", "file": "veltman.RData", "class": [ "data.frame" ], "fields": [ "Clone", "Chromosome", "Array", "gene", "LogRatio", "PosOrder", "PosBase" ], "rows": 1747, "table": true, "tojson": true }, { "name": "P9", "title": "Public CGH data of Veltman", "object": "veltman", "file": "veltman.RData", "class": [ "data.frame" ], "fields": [ "Clone", "Chromosome", "Array", "gene", "LogRatio", "PosOrder", "PosBase" ], "rows": 1747, "table": true, "tojson": true } ], "_help": [ { "page": "bladder", "title": "Bladder cancer CGH data", "topics": [ "array1", "array2", "array3" ] }, { "page": "arrayCGH", "title": "Object of Class arrayCGH", "topics": [ "arrayCGH" ] }, { "page": "arrayPersp", "title": "Perspective image of microarray spots statistic", "topics": [ "arrayPersp", "arrayPersp.arrayCGH", "arrayPersp.default" ] }, { "page": "arrayPlot", "title": "Spatial image of microarray spots statistic", "topics": [ "arrayPlot", "arrayPlot.arrayCGH", "arrayPlot.default" ] }, { "page": "as.data.frame.profileCGH", "title": "profileCGH consercion", "topics": [ "as.data.frame.profileCGH" ] }, { "page": "as.profileCGH", "title": "Create an object of class profileCGH", "topics": [ "as.profileCGH", "as.profileCGH.data.frame" ] }, { "page": "ChrNumeric", "title": "Convert chromosome into numeric values", "topics": [ "ChrNumeric" ] }, { "page": "ColorBar", "title": "Calibration bar for color images", "topics": [ "ColorBar" ] }, { "page": "cytoband", "title": "Cytogenetic banding", "topics": [ "cytoband" ] }, { "page": "daglad", "title": "Analysis of array CGH data", "topics": [ "daglad", "daglad.profileCGH" ] }, { "page": "glad", "title": "Analysis of array CGH data", "topics": [ "glad", "glad.profileCGH" ] }, { "page": "hclust", "title": "Hierarchical Clustering", "topics": [ "hclustglad" ] }, { "page": "kernel", "title": "Kernelpen function", "topics": [ "kernelpen" ] }, { "page": "myPalette", "title": "Microarray color palette", "topics": [ "myPalette" ] }, { "page": "plotProfile", "title": "Plot genomic profile and cytogenetic banding", "topics": [ "plotProfile", "plotProfile.profileCGH" ] }, { "page": "profileCGH", "title": "Objects of Class profileCGH and profileChr", "topics": [ "profileCGH", "profileChr" ] }, { "page": "snijders", "title": "Public CGH data of Snijders", "topics": [ "gm00143", "gm01524", "gm01535", "gm01750", "gm02948", "gm03134", "gm03563", "gm03576", "gm04435", "gm05296", "gm07081", "gm07408", "gm10315", "gm13031", "gm13330" ] }, { "page": "veltman", "title": "Public CGH data of Veltman", "topics": [ "P20", "P9" ] } ], "_rundeps": [ "aws", "awsMethods", "gsl" ], "_sysdeps": [ { "shlib": "libgsl", "package": "libgsl27", "headers": "libgsl-dev", "source": "gsl", "version": "2.7.1+dfsg-6ubuntu2", "name": "gsl", "homepage": "https://www.gnu.org/software/gsl", "description": "GNU Scientific Library (GSL) -- library package" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "GLAD.Rnw", "filename": "GLAD.pdf", "title": "GLAD", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:52:39", "modified": "2020-04-15 14:47:14", "commits": 2 } ], "_score": 6.17260293120986, "_indexed": false, "_nocasepkg": "glad", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/GLAD", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.76.0", "date": "2026-05-24T06:37:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "525084405715247cdffdc9a1af43da6fda1b7f83ba6918a6e0f111953dddc96d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.7.0", "os": "linux", "version": "2.76.0", "date": "2026-05-24T06:38:23.000Z", "distro": "noble", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "532ef03081d0cda640db67154dfa6c04aae8c47d1d6ac65179ecb7129754edc6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "linux", "version": "2.76.0", "date": "2026-05-24T06:38:10.000Z", "distro": "noble", "arch": "aarch64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "e4d69cd17b948e3ea8290ba55dff5d4e061dd883063a23baa648ee5558cb4001", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "linux", "version": "2.76.0", "date": "2026-05-24T06:38:09.000Z", "distro": "noble", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "47019087c001d81dbf5bcedad7a74edddf846927573d08dbf58abb127fc128d4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.5.3", "os": "mac", "version": "2.76.0", "date": "2026-05-24T06:37:13.000Z", "arch": "aarch64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "76ae52124773987ae9a8064bbe76555ac9feffad8f33ff89babb5422c307ab06", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.5.3", "os": "mac", "version": "2.76.0", "date": "2026-05-24T06:38:29.000Z", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "e773822379d36e101f3a366c81aa8083899403a112e56a6da59973795e48eadf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "mac", "version": "2.76.0", "date": "2026-05-24T06:37:02.000Z", "arch": "aarch64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "c667dbd8d5a2bbd57b6316e028067e6f6c5e3949f7f869565c6f722670378d29", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "mac", "version": "2.76.0", "date": "2026-05-24T06:38:16.000Z", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "312d57bd96ca40c5f4e239c4d5c06b1273813a8d6689fcdf84a05a9360ea9f30", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "wasm", "version": "2.76.0", "date": "2026-05-24T06:37:37.000Z", "arch": "emscripten", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "def85e6792a9b0491586bdea0333a8132034bb69a0de09f87cc627790393e647", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.7.0", "os": "win", "version": "2.76.0", "date": "2026-05-24T06:37:06.000Z", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "26bb9827a32b96fb10490ebfbb256ebf270fb4d950711ae771e5ee60344ffdf8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.5.3", "os": "win", "version": "2.76.0", "date": "2026-05-24T06:36:41.000Z", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "b4f3eaea57017c87f38187a1dd7aa70851efd7dbca1fff6dd4a7fa821da9ba56", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" }, { "r": "4.6.0", "os": "win", "version": "2.76.0", "date": "2026-05-24T06:37:21.000Z", "arch": "x86_64", "commit": "36043955d9a38510ccce25e6da64498c9d83dfe5", "fileid": "7b01b73192a438963173d516eb8fcda85f4baa1aaf7248ad0b209c6c7fdd358e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354081234" } ] }