{ "_id": "6a1efbadb401979e73418bf0", "Package": "ruv", "Title": "Detect and Remove Unwanted Variation using Negative Controls", "Description": "Implements the 'RUV' (Remove Unwanted Variation)\nalgorithms. These algorithms attempt to adjust for systematic\nerrors of unknown origin in high-dimensional data. The\nalgorithms were originally developed for use with genomic data,\nespecially microarray data, but may be useful with other types\nof high-dimensional data as well. These algorithms were\nproposed in Gagnon-Bartsch and Speed (2012)\n, Gagnon-Bartsch, Jacob and Speed\n(2013), and Molania, et. al. (2019) .\nThe algorithms require the user to specify a set of negative\ncontrol variables, as described in the references. The\nalgorithms included in this package are 'RUV-2', 'RUV-4',\n'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with\nvarious supporting algorithms.", "Version": "0.9.7.1", "Date": "2019-08-30", "Author": "Johann Gagnon-Bartsch ", "Maintainer": "Johann Gagnon-Bartsch ", "License": "GPL", "URL": "http://www-personal.umich.edu/~johanngb/ruv/", "LazyLoad": "yes", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-18 10:28:28 UTC", "User": "root" }, "Repository": "https://johanngb.r-universe.dev", "Date/Publication": "2019-08-30 20:50:02 UTC", "RemoteUrl": "https://github.com/cran/ruv", "RemoteRef": "HEAD", "RemoteSha": "992316897d5fd6df5702912f4c45c4ea7b4935be", "MD5sum": "cd390344a1aee6c7fe8257aa18d5352b", "_user": "johanngb", "_type": "src", "_file": "ruv_0.9.7.1.tar.gz", "_fileid": "212f7a14c9e37c059b8795e77b9b9083080f9e5842672f54537d6e7a2842a6fe", "_filesize": 239989, "_sha256": "212f7a14c9e37c059b8795e77b9b9083080f9e5842672f54537d6e7a2842a6fe", "_created": "2026-05-18T10:28:28.000Z", "_published": "2026-06-02T15:50:05.252Z", "_distro": "noble", "_jobs": [ { "job": 79112726603, "time": 132, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7055412278" }, { "job": 79112726398, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7055415601" }, { "job": 79112726987, "time": 117, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7055407540" }, { "job": 79112727895, "time": 128, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7055411012" }, { "job": 79112727454, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7055436481" }, { "job": 79112727029, "time": 407, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7055491582" }, { "job": 79112726940, "time": 219, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7055427886" }, { "job": 79112726845, "time": 289, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7055469937" }, { "job": 79112725782, "time": 161, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7055366760" }, { "job": 79112725969, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7362813366" }, { "job": 79112726553, "time": 106, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7055403873" }, { "job": 79112726979, "time": 119, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7055408190" }, { "job": 79112727046, "time": 95, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7055400258" } ], "_buildurl": "https://github.com/r-universe/johanngb/actions/runs/26027807877", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/ruv", "_commit": { "id": "992316897d5fd6df5702912f4c45c4ea7b4935be", "author": "Johann Gagnon-Bartsch ", "committer": "cran-robot ", "message": "version 0.9.7.1\n", "time": 1567198202 }, "_maintainer": { "name": "Johann Gagnon-Bartsch", "email": "johanngb@umich.edu", "login": "johanngb", "description": "I am an Assistant Professor in the Department of Statistics at the University of Michigan. ", "uuid": 15433339 }, "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "shiny", "role": "Suggests" }, { "package": "colourpicker", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 13, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "johanngb", "count": 3, "uuid": 15433339 } ], "_userbio": { "uuid": 15433339, "type": "user", "name": "Johann Gagnon-Bartsch", "description": "I am an Assistant Professor in the Department of Statistics at the University of Michigan. " }, "_downloads": { "count": 1897, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ruv" }, "_mentions": 4, "_searchresults": 100, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ruv.html", "manual.pdf" ], "_realowner": "johanngb", "_cranurl": false, "_releases": [ { "version": "0.9.4", "date": "2014-10-24" }, { "version": "0.9.5", "date": "2015-05-20" }, { "version": "0.9.6", "date": "2015-07-18" }, { "version": "0.9.7", "date": "2018-03-12" }, { "version": "0.9.7.1", "date": "2019-08-30" } ], "_exports": [ "collapse.replicates", "design.matrix", "get_empirical_variances", "getK", "google_search", "inputcheck1", "invvar", "projectionplotvariables", "randinvvar", "replicate.matrix", "residop", "ruv_cancorplot", "ruv_ecdf", "ruv_hist", "ruv_projectionplot", "ruv_rankplot", "ruv_residuals", "ruv_rle", "ruv_scree", "ruv_shiny", "ruv_summary", "ruv_svdgridplot", "ruv_svdplot", "ruv_varianceplot", "ruv_volcano", "RUV1", "RUV2", "RUV4", "RUVI", "RUVIII", "RUVinv", "RUVrinv", "sigmashrink", "variance_adjust" ], "_help": [ { "page": "ruv-package", "title": "Detect and Remove Unwanted Variation using Negative Controls", "topics": [ "ruv-package", "ruv" ] }, { "page": "collapse.replicates", "title": "Collapse Replicates", "topics": [ "collapse.replicates" ] }, { "page": "design.matrix", "title": "Design Matrix", "topics": [ "design.matrix" ] }, { "page": "get_empirical_variances", "title": "Get empirical variances", "topics": [ "get_empirical_variances" ] }, { "page": "getK", "title": "Get K", "topics": [ "getK" ] }, { "page": "google_search", "title": "Google Search URL", "topics": [ "google_search" ] }, { "page": "inputcheck1", "title": "Input Check One", "topics": [ "inputcheck1" ] }, { "page": "invvar", "title": "Inverse Method Variances", "topics": [ "invvar" ] }, { "page": "projectionplotvariables", "title": "Projection Plot Variables", "topics": [ "projectionplotvariables" ] }, { "page": "randinvvar", "title": "(Randomization) Inverse Method Variances", "topics": [ "randinvvar" ] }, { "page": "replicate.matrix", "title": "Replicate (Mapping) Matrix", "topics": [ "replicate.matrix" ] }, { "page": "residop", "title": "Residual Operator", "topics": [ "residop" ] }, { "page": "ruv_cancorplot", "title": "RUV Canonical Correlation Plot", "topics": [ "ruv_cancorplot" ] }, { "page": "ruv_ecdf", "title": "RUV P-value Empirical CDF Plot", "topics": [ "ruv_ecdf" ] }, { "page": "ruv_hist", "title": "RUV P-value Histogram Plot", "topics": [ "ruv_hist" ] }, { "page": "ruv_projectionplot", "title": "RUV Projection Plot", "topics": [ "ruv_projectionplot" ] }, { "page": "ruv_rankplot", "title": "RUV Rank Plot", "topics": [ "ruv_rankplot" ] }, { "page": "ruv_residuals", "title": "RUV Residuals", "topics": [ "ruv_residuals" ] }, { "page": "ruv_rle", "title": "RUV RLE Plot", "topics": [ "ruv_rle" ] }, { "page": "ruv_scree", "title": "RUV Scree Plot", "topics": [ "ruv_scree" ] }, { "page": "ruv_shiny", "title": "RUV Shiny App", "topics": [ "ruv_shiny" ] }, { "page": "ruv_summary", "title": "RUV Summary", "topics": [ "ruv_summary" ] }, { "page": "ruv_svdgridplot", "title": "RUV SVD Grid Plot", "topics": [ "ruv_svdgridplot" ] }, { "page": "ruv_svdplot", "title": "RUV SVD Plot", "topics": [ "ruv_svdplot" ] }, { "page": "ruv_varianceplot", "title": "RUV Variance Plot", "topics": [ "ruv_varianceplot" ] }, { "page": "ruv_volcano", "title": "RUV Volcano Plot", "topics": [ "ruv_volcano" ] }, { "page": "RUV2", "title": "Remove Unwanted Variation, 2-step", "topics": [ "RUV2" ] }, { "page": "RUV4", "title": "Remove Unwanted Variation, 4-step", "topics": [ "RUV4" ] }, { "page": "RUVI", "title": "RUV-I", "topics": [ "RUV1", "RUVI" ] }, { "page": "RUVIII", "title": "RUV-III", "topics": [ "RUVIII" ] }, { "page": "RUVinv", "title": "Remove Unwanted Variation, inverse method", "topics": [ "RUVinv" ] }, { "page": "RUVrinv", "title": "Remove Unwanted Variation, ridged inverse method", "topics": [ "RUVrinv" ] }, { "page": "sigmashrink", "title": "Empirical Bayes shrinkage estimate of sigma^2", "topics": [ "sigmashrink" ] }, { "page": "variance_adjust", "title": "Adjust Estimated Variances", "topics": [ "variance_adjust" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 4.772221924907106, "_indexed": true, "_nocasepkg": "ruv", "_universes": [ "johanngb" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.9.7.1", "date": "2026-05-18T10:30:38.000Z", "distro": "noble", "arch": "aarch64", "commit": "992316897d5fd6df5702912f4c45c4ea7b4935be", "fileid": "b0749aeaa756be22bcaeb545a0b5a319e607bc71bdd29a2849efe0e589aa8916", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/johanngb/actions/runs/26027807877" }, { "r": 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