RUVSeq-package: Remove Unwanted Variation from RNA-Seq Data

In RUVSeq: Remove Unwanted Variation from RNA-Seq Data

Description

This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

Details

Package:	RUVSeq
Type:	Package
Version:	0.99.1
Date:	2014-04-15
License:	Artistic-2.0

The RUVg function implements the RUVg normalization procedure of Risso et al. (2014), by using control genes to remove unwanted variation from the RNA-Seq read counts.

See also RUVr and RUVs for the "residual" and "sample" methods, based, respectively, on residuals (e.g., deviance residuals from a first-pass GLM regression of the unnormalized counts on the covariates of interest) and replicate/negative control samples for which the covariates of interest are constant.

Author(s)

Davide Risso and Sandrine Dudoit

Maintainer: Davide Risso <[e-mail]>

References

D. Risso, J. Ngai, T. P. Speed, and S. Dudoit. Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology, 2014. (In press).

D. Risso, J. Ngai, T. P. Speed, and S. Dudoit. The role of spike-in standards in the normalization of RNA-Seq. In D. Nettleton and S. Datta, editors, Statistical Analysis of Next Generation Sequence Data. Springer, 2014. (In press).

See Also

RUVg, RUVr, RUVs

RUVSeq documentation built on Nov. 8, 2020, 8:02 p.m.