RUVSeq

DOI: 10.18129/B9.bioc.RUVSeq    

This is the development version of RUVSeq; for the stable release version, see RUVSeq.

Remove Unwanted Variation from RNA-Seq Data

Bioconductor version: Development (3.15)

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>

Citation (from within R, enter citation("RUVSeq")):

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RUVSeq")

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

Documentation

PDF   Reference Manual

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software
Version 1.29.0
In Bioconductor since BioC 3.0 (R-3.1) (7 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
Windows Binary
macOS 10.13 (High Sierra)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: