RUVSeq

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see RUVSeq.

Remove Unwanted Variation from RNA-Seq Data

Bioconductor version: 3.19

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 "4.4") 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")

RUVSeq: Remove Unwanted Variation from RNA-Seq Data HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software

Version 1.38.0

In Bioconductor since BioC 3.0 (R-3.1) (10 years)

License Artistic-2.0

Depends Biobase, EDASeq(>= 1.99.1), edgeR

Imports methods, MASS

System Requirements

URL https://github.com/drisso/RUVSeq

Bug Reports https://github.com/drisso/RUVSeq/issues

Suggests BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2

Linking To

Enhances

Depends On Me octad, rnaseqGene

Imports Me consensusDE, ribosomeProfilingQC, scone, standR

Suggests Me DEScan2, NanoTube

Links To Me

Build Report Build Report

Package Archives

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

Source Package RUVSeq_1.38.0.tar.gz

Windows Binary (x86_64) RUVSeq_1.38.0.zip

macOS Binary (x86_64) RUVSeq_1.38.0.tgz

macOS Binary (arm64) RUVSeq_1.38.0.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/

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