{ "_id": "6a4995e974ff1be5edd78c14", "Package": "MANOR", "Version": "1.85.0", "Date": "2024-03-12", "Title": "CGH Micro-Array NORmalization", "Description": "Importation, normalization, visualization, and quality\ncontrol functions to correct identified sources of variability\nin array-CGH experiments.", "Author": "Pierre Neuvial , Philippe Hupé\n", "Maintainer": "Pierre Neuvial ", "License": "GPL-2", "VignetteBuilder": "knitr", "URL": "http://bioinfo.curie.fr/projects/manor/index.html", "BugReports": "https://github.com/pneuvial/MANOR/issues", "Encoding": "UTF-8", "biocViews": "Microarray, TwoChannel, DataImport, QualityControl,\nPreprocessing, CopyNumberVariation, Normalization", "Config/pak/sysreqs": "libgsl0-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:31:27 UTC", "RemoteUrl": "https://github.com/bioc/MANOR", "RemoteRef": "HEAD", "RemoteSha": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-04 23:18:02 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "MANOR_1.85.0.tar.gz", "_fileid": "https://r2.ropensci.org/2ade86ebac00266f947a407a66034fd96528cd475f62ae354e8296bca7615891", "_filesize": 636456, "_sha256": "2ade86ebac00266f947a407a66034fd96528cd475f62ae354e8296bca7615891", "_expires": "2026-10-12T23:23:19.000Z", "_created": "2026-07-04T23:18:02.000Z", "_published": "2026-07-04T23:23:21.524Z", "_bioccheck": { "error": 2, "warning": 1, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940", "_status": "failure", "_upstream": "https://github.com/bioc/MANOR", "_commit": { "id": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379487 }, "_maintainer": { "name": "Pierre Neuvial", "email": "pierre.neuvial@math.cnrs.fr", "login": "pneuvial", "orcid": "0000-0003-3584-9998", "description": "", "uuid": 7895899 }, "_distro": "resolute", "_jobs": [ { "job": 85175085531, "time": 164, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8086328749" }, { "job": 85175085506, "time": 175, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "8086330155" }, { "job": 85175085517, "time": 151, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8086327310" }, { "job": 85175085544, "time": 147, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8086327360" }, { "job": 85175085511, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8086327220" }, { "job": 85175085522, "time": 86, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8086338772" }, { "job": 85175085526, "time": 157, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "8086332373" }, { "job": 85175085527, "time": 93, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8086340293" }, { "job": 85175085515, "time": 198, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8086336606" }, { "job": 85174926158, "time": 170, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8086311375" }, { "job": 85175085491, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086322579" }, { "job": 85175085520, "time": 96, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8086321401" }, { "job": 85175085514, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8086320571" }, { "job": 85175085524, "time": 97, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8086321385" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "GLAD", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.85.0", "bioc": "3.24" }, { "branch": "release", "version": "1.84.0", "bioc": "3.23" } ], "_topics": [ "microarray", "twochannel", "dataimport", "qualitycontrol", "preprocessing", "copynumbervariation", "normalization" ], "_stars": 0, "_contributors": [ { "user": "henrikbengtsson", "count": 29, "uuid": 1616850 }, { "user": "dtenenba", "count": 25, "uuid": 2286826 }, { "user": "pneuvial", "count": 10, "uuid": 7895899 }, { "user": "nturaga", "count": 8, "uuid": 2746443 }, { "user": "lshep", "count": 4, "uuid": 18724380 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "jmacdon", "count": 1, "uuid": 5940924 }, { "user": "pekkarr", "count": 1, "uuid": 40121471 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 7, "_devurl": "https://github.com/pneuvial/manor", "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MANOR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pneuvial/manor", "_realowner": "bioc", "_cranurl": false, "_exports": [ "add.lines", "arrayCGH2txt", "arrayTrend", "arrayTrend.arrayCGH", "arrayTrend.default", "center", "check.names", "chrom", "cv", "detectSB", "detectSB.arrayCGH", "flag.aggregate.arrayCGH", "flag.arrayCGH", "flag.summary", "flag.summary.arrayCGH", "flag.summary.default", "genome.plot", "genome.plot.arrayCGH", "genome.plot.default", "getChromosomeArm", "html.report", "html.report.arrayCGH", "html.report.default", "import", "import.default.aux", "import.gpr.aux", "import.spot.aux", "intensity.plot", "my.aggregate.data.frame", "nem", "nem.arrayCGH", "nem.default", "norm", "norm.arrayCGH", "print.flag", "qscore.arrayCGH", "qscore.summary.arrayCGH", "rename", "report.plot", "report.plot.arrayCGH", "report.plot.default", "sort.arrayCGH", "to.flag", "to.qscore", "w" ], "_datasets": [ { "name": "amplicon.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "chromosome.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "clone.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "control.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "dapi.snr.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "dyn.x.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "dyn.y.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "dynamics.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "edge", "title": "Examples of array-CGH data with spatial artifacts", "object": "spatial", "file": "spatial.RData", "class": [ "arrayCGH" ], "fields": [], "table": false, "tojson": false }, { "name": "edge.norm", "title": "Examples of array-CGH data with spatial artifacts", "object": "spatial", "file": "spatial.RData", "class": [ "arrayCGH" ], "fields": [], "table": false, "tojson": false }, { "name": "global.spatial.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "gradient", "title": "Examples of array-CGH data with spatial artifacts", "object": "spatial", "file": "spatial.RData", "class": [ "arrayCGH" ], "fields": [], "table": false, "tojson": false }, { "name": "gradient.norm", "title": "Examples of array-CGH data with spatial artifacts", "object": "spatial", "file": "spatial.RData", "class": [ "arrayCGH" ], "fields": [], "table": false, "tojson": false }, { "name": "intensity.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "local.spatial.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "num.chromosome.flag", "title": "Internal Functions for MANOR Package", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "pct.clone.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "pct.replicate.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "pct.spot.before.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "pct.spot.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "position.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "ref.snr.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "rep.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "replicate.aux", "title": "Internal Functions for MANOR Package", "object": "flags", "file": "flags.RData", "class": [ "function" ], "fields": [], "table": false, "tojson": true }, { "name": "replicate.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "smoothness.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false }, { "name": "SNR.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "spatial.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "spot.corr.flag", "title": "Internal Functions for MANOR Package", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "spot.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "unique.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "val.mark.flag", "title": "Examples of flag objects to apply to CGH arrays", "object": "flags", "file": "flags.RData", "class": [ "flag" ], "fields": [], "table": false, "tojson": false }, { "name": "var.replicate.qscore", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "object": "qscores", "file": "qscores.RData", "class": [ "qscore" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "arrayTrend", "title": "Spatial trend of microarray spots statistic", "topics": [ "arrayTrend", "arrayTrend.arrayCGH", "arrayTrend.default" ] }, { "page": "detectSB", "title": "Spatial bias detection", "topics": [ "detectSB", "detectSB.arrayCGH", "detectSB.default" ] }, { "page": "flag.arrayCGH", "title": "Apply a flag to an arrayCGH", "topics": [ "flag", "flag.arrayCGH" ] }, { "page": "flag.summary", "title": "Summarize information about flags after array normalization", "topics": [ "flag.summary", "flag.summary.arrayCGH", "flag.summary.default" ] }, { "page": "flags", "title": "Examples of flag objects to apply to CGH arrays", "topics": [ "amplicon.flag", "chromosome.flag", "control.flag", "dapi.snr.flag", "flags", "global.spatial.flag", "intensity.flag", "local.spatial.flag", "position.flag", "ref.snr.flag", "rep.flag", "replicate.flag", "SNR.flag", "spatial.flag", "spot.flag", "unique.flag", "val.mark.flag" ] }, { "page": "genome.plot", "title": "Pan-genomic representation of a normalized arrayCGH", "topics": [ "genome.plot", "genome.plot.arrayCGH", "genome.plot.default" ] }, { "page": "html.report", "title": "Generate an HTML report of array normalization", "topics": [ "html.report", "html.report.arrayCGH", "html.report.default" ] }, { "page": "import", "title": "Import raw file to an arrayCGH object", "topics": [ "import", "import.default.aux", "import.gpr.aux", "import.spot.aux" ] }, { "page": "nem", "title": "Spatial Classification by EM algorithm", "topics": [ "nem", "nem.arrayCGH", "nem.default" ] }, { "page": "norm", "title": "Normalize an object of type arrayCGH", "topics": [ "MANOR", "manor", "norm", "norm.arrayCGH" ] }, { "page": "qscore", "title": "Create an object of type qscore", "topics": [ "qscore", "to.qscore" ] }, { "page": "qscore.arrayCGH", "title": "arrayCGH quality score", "topics": [ "qscore.arrayCGH" ] }, { "page": "qscore.summary", "title": "Compute quality scores for a given arrayCGH object", "topics": [ "qscore.summary", "qscore.summary.arrayCGH" ] }, { "page": "qscores", "title": "Examples of qscore objects (quality scores) to apply to CGH arrays", "topics": [ "clone.qscore", "dyn.x.qscore", "dyn.y.qscore", "dynamics.qscore", "pct.clone.qscore", "pct.replicate.qscore", "pct.spot.before.qscore", "pct.spot.qscore", "smoothness.qscore", "var.replicate.qscore" ] }, { "page": "report.plot", "title": "Array image and a genomic representation of a normalized arrayCGH", "topics": [ "report.plot", "report.plot.arrayCGH", "report.plot.default" ] }, { "page": "sort", "title": "Sorting for normalized arrayCGH objects", "topics": [ "sort", "sort.arrayCGH" ] }, { "page": "spatial", "title": "Examples of array-CGH data with spatial artifacts", "topics": [ "edge", "edge.norm", "edge.txt", "gradient", "gradient.gpr", "gradient.norm", "spatial" ] }, { "page": "to.flag", "title": "Create an object of type flag", "topics": [ "to.flag" ] } ], "_readme": "https://github.com/bioc/MANOR/raw/HEAD/README.md", "_rundeps": [ "aws", "awsMethods", "GLAD", "gsl" ], "_score": 4.799340549453581, "_indexed": true, "_nocasepkg": "manor", "_universes": [ "bioc", "pneuvial" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.85.0", "date": "2026-07-04T23:21:07.000Z", "distro": "resolute", "arch": "aarch64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/e77addefb799bae21f71c8a294c038be256cb37afcca1581dcfedf2c753a5ecc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.7.0", "os": "linux", "version": "1.85.0", "date": "2026-07-04T23:20:36.000Z", "distro": "resolute", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/0f4453355648b10eb4321bcd6575dfa291a587665facc98b72b9282ecbe0b131", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.1", "os": "linux", "version": "1.85.0", "date": "2026-07-04T23:20:41.000Z", "distro": "resolute", "arch": "aarch64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/d4c9454bd0e1791134270bcf66c1e7ecc58ab3c4259076a631c90eba5de9d461", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.1", "os": "linux", "version": "1.85.0", "date": "2026-07-04T23:20:35.000Z", "distro": "resolute", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/5d86eef405f51e51578f52e3d5cf5e289553e7399c9db1614e1441c23e5b2317", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.5.3", "os": "mac", "version": "1.85.0", "date": "2026-07-04T23:22:26.000Z", "arch": "aarch64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/290cef917f2beaebcbdc7f6de19f0929200108ba4b9911117233c90a4b3fb09e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.5.3", "os": "mac", "version": "1.85.0", "date": "2026-07-04T23:21:12.000Z", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/11ff98a833bd237487034f5ae21e72cc01fe8cc20dd8fe6046f9a316b54969db", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.1", "os": "mac", "version": "1.85.0", "date": "2026-07-04T23:22:39.000Z", "arch": "aarch64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/f4a7a8c148206c92f1e695724a791ee6511aa6ea9a88a699322251bdac15ddb1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.1", "os": "mac", "version": "1.85.0", "date": "2026-07-04T23:21:28.000Z", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/78d4507c372b3b617b7966dfd896e54a0f8561ea2051d0742c0c51cfccb4247c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.0", "os": "wasm", "version": "1.85.0", "date": "2026-07-04T23:20:11.000Z", "arch": "emscripten", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/fcb599c368dfa4518a35a52f46169c8a224692e49d90bb80a7dc91c32431756f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.7.0", "os": "win", "version": "1.85.0", "date": "2026-07-04T23:19:21.000Z", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/01f3afe4affe6314b4be35ce9155366946494dd420de53f6be4ae6b55bb18eb4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.5.3", "os": "win", "version": "1.85.0", "date": "2026-07-04T23:19:17.000Z", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/f00d65f88f7f939749a0aa5341a7124d6ed8b9418d234265e495dff92393e149", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" }, { "r": "4.6.1", "os": "win", "version": "1.85.0", "date": "2026-07-04T23:19:26.000Z", "arch": "x86_64", "commit": "609a70df8a1877a4b2431fbb09fbf495cb6db1f9", "fileid": "https://r2.ropensci.org/bfd6cdbb31aca9f448d2291eb6b2f79f75629a1e75ff9cf6508e6622ecd1317e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722765940" } ] }