To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RUVSeq")
In most cases, you don't need to download the package archive at all.
RUVSeq
Remove Unwanted Variation from RNA-Seq Data
Bioconductor version: 3.0
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 and Sandrine Dudoit
Maintainer: Davide Risso <risso.davide at gmail.com>
Citation (from within R,
enter citation("RUVSeq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RUVSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RUVSeq")
| R Script | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Preprocessing, RNASeq, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | EDASeq(>= 1.99.1), edgeR |
| Imports | methods, MASS |
| LinkingTo | |
| Suggests | BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RUVSeq_1.0.0.tar.gz |
| Windows Binary | RUVSeq_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | RUVSeq_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | RUVSeq_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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