RUVSeq
Remove Unwanted Variation from RNA-Seq Data
Bioconductor version: Release (3.20)
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software |
| Version | 1.40.0 |
| 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 |
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_1.40.0.tar.gz |
| Windows Binary (x86_64) | RUVSeq_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | RUVSeq_1.40.0.tgz |
| macOS Binary (arm64) | RUVSeq_1.39.0.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 |