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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
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

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: MBECS, missMethyl, PhosR, scMerge, standR
Reverse suggests: NanoTube

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ruv to link to this page.

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.