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ruv
View on CRAN: Click
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Download and install ruv package within the R console
Install from CRAN:
install.packages("ruv")
Install from Github:
library("remotes")
install_github("cran/ruv")
Install by package version:
library("remotes")
install_version("ruv", "0.9.7.1")
Attach the package and use:
library("ruv")
Maintained by
Johann Gagnon-Bartsch
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-10-24
Latest Update: 2019-08-30
Description:
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.
How to cite:
Johann Gagnon-Bartsch (2014). ruv: Detect and Remove Unwanted Variation using Negative Controls. R package version 0.9.7.1, https://cran.r-project.org/web/packages/ruv
Previous versions and publish date:
Other packages that cited ruv R package
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Other R packages that ruv depends,
imports, suggests or enhances
Functions, R codes and Examples using
the ruv R package
Some associated functions: RUV2 . RUV4 . RUVI . RUVIII . RUVinv . RUVrinv . collapse.replicates . design.matrix . getK . get_empirical_variances . google_search . inputcheck1 . invvar . projectionplotvariables . randinvvar . replicate.matrix . residop . ruv-package . 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 . sigmashrink . variance_adjust .
Some associated R codes: RUV1.R . RUV2.R . RUV4.R . RUVI.R . RUVIII.R . RUVinv.R . RUVrinv.R . check.X.col.R . check.X.col_2.R . check.factor.R . check.ggplot.R . check.gridExtra.R . check.power.R . collapse.replicates.R . design.column.R . design.matrix.R . getK.R . getKcutoff.R . get_empirical_variances.R . getinvsvd.R . getsizeratios.R . google_search.R . inputcheck1.R . invvar.R . lsvd.R . momentintegral.R . projectionplotvariables.R . randinvvar.R . replicate.matrix.R . residop.R . ruv_cancorplot.R . ruv_ecdf.R . ruv_hist.R . ruv_projectionplot.R . ruv_rankplot.R . ruv_residuals.R . ruv_rle.R . ruv_scree.R . ruv_shiny.R . ruv_summary.R . ruv_svdgridplot.R . ruv_svdplot.R . ruv_varianceplot.R . ruv_volcano.R . sigmashrink.R . tological.R . variance_adjust.R . Full ruv package functions and examples
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