ruv: Detect and Remove Unwanted Variation using Negative Controls

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
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

Documentation:

Reference manual:

ruv.pdf

Downloads:

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 dependencies:

Reverse imports:	cate, MBECS, missMethyl, PhosR, scMerge, standR
Reverse suggests:	NanoTube, RUVIIIC

Linking:

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