RUVSeq

DOI: 10.18129/B9.bioc.RUVSeq  

Remove Unwanted Variation from RNA-Seq Data

Bioconductor version: Release (3.16)

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 "4.2") and enter:

if (!require("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	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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	octad, rnaseqGene
Imports Me	consensusDE, ribosomeProfilingQC, scone, standR
Suggests Me	DEScan2, NanoTube
Links To Me
Build Report

Package Archives

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

Source Package	RUVSeq_1.32.0.tar.gz
Windows Binary	RUVSeq_1.32.0.zip
macOS Binary (x86_64)	RUVSeq_1.32.0.tgz
macOS Binary (arm64)	RUVSeq_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RUVSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RUVSeq
Bioc Package Browser	https://code.bioconductor.org/browse/RUVSeq/
Package Short Url	https://bioconductor.org/packages/RUVSeq/
Package Downloads Report	Download Stats