EDASeq

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Development (3.0)

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

Author: Davide Risso and Sandrine Dudoit

Maintainer: Davide Risso <risso.davide at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("EDASeq")

To cite this package in a publication, start R and enter:

    citation("EDASeq")

Documentation

PDF R Script EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.99.1
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends Biobase(>= 2.15.1), ShortRead(>= 1.11.42)
Imports methods, graphics, BiocGenerics, IRanges(>= 1.13.9), DESeq, aroma.light, Rsamtools(>= 1.5.75)
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR
System Requirements
URL
Depends On Me metaseqR
Imports Me
Suggests Me HTSFilter, oneChannelGUI

Package Downloads

Package Source EDASeq_1.99.1.tar.gz
Windows Binary EDASeq_1.99.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) EDASeq_1.99.1.tgz
Mac OS X 10.9 (Mavericks)
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