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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 (3.19)

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")

# 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

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

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
See More
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_1.37.0.tar.gz
Windows Binary RUVSeq_1.37.0.zip
macOS Binary (x86_64) RUVSeq_1.37.0.tgz
macOS Binary (arm64) RUVSeq_1.37.0.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