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Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.
Version: | 0.9.7.1 |
Imports: | stats, ggplot2, scales, gridExtra |
Suggests: | shiny, colourpicker |
Published: | 2019-08-30 |
DOI: | 10.32614/CRAN.package.ruv |
Author: | Johann Gagnon-Bartsch |
Maintainer: | Johann Gagnon-Bartsch <johanngb at umich.edu> |
License: | GPL-2 | GPL-3 [expanded from: GPL] |
URL: | http://www-personal.umich.edu/~johanngb/ruv/ |
NeedsCompilation: | yes |
CRAN checks: | ruv results |
Reference manual: | ruv.pdf |
Package source: | ruv_0.9.7.1.tar.gz |
Windows binaries: | r-devel: ruv_0.9.7.1.zip, r-release: ruv_0.9.7.1.zip, r-oldrel: ruv_0.9.7.1.zip |
macOS binaries: | r-release (arm64): ruv_0.9.7.1.tgz, r-oldrel (arm64): ruv_0.9.7.1.tgz, r-release (x86_64): ruv_0.9.7.1.tgz, r-oldrel (x86_64): ruv_0.9.7.1.tgz |
Old sources: | ruv archive |
Reverse imports: | MBECS, missMethyl, PhosR, scMerge, standR |
Reverse suggests: | NanoTube |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.