RUVSeq

DOI: 10.18129/B9.bioc.RUVSeq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RUVSeq.

Remove Unwanted Variation from RNA-Seq Data

Bioconductor version: 3.8

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 "3.5") 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 1.16.1
In Bioconductor since BioC 3.0 (R-3.1) (4.5 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, 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_1.16.1.tar.gz
Windows Binary RUVSeq_1.16.1.zip
Mac OS X 10.11 (El Capitan) RUVSeq_1.16.1.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 http://bioconductor.org/packages/RUVSeq/
Package Downloads Report Download Stats

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