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>

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

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 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
Package Short Url https://bioconductor.org/packages/RUVSeq/
Package Downloads Report Download Stats

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