RUVSeq

DOI: 10.18129/B9.bioc.RUVSeq    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RUVSeq.

Remove Unwanted Variation from RNA-Seq Data

Bioconductor version: 3.12

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

Author: Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]

Maintainer: Davide Risso <risso.davide at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RUVSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RUVSeq")

 

PDF	R Script	RUVSeq: Remove Unwanted Variation from RNA-Seq Data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software
Version	1.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (6.5 years)
License	Artistic-2.0
Depends	Biobase, EDASeq(>= 1.99.1), edgeR
Imports	methods, MASS
LinkingTo
Suggests	BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
SystemRequirements
Enhances
URL	https://github.com/drisso/RUVSeq
BugReports	https://github.com/drisso/RUVSeq/issues
Depends On Me	rnaseqGene
Imports Me	consensusDE, ribosomeProfilingQC, scone
Suggests Me	DEScan2
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RUVSeq_1.24.0.tar.gz
Windows Binary	RUVSeq_1.24.0.zip
macOS 10.13 (High Sierra)	RUVSeq_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RUVSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RUVSeq
Package Short Url	https://bioconductor.org/packages/RUVSeq/
Package Downloads Report	Download Stats