To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EDASeq")

In most cases, you don't need to download the package archive at all.

EDASeq

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see EDASeq.

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: 3.1

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EDASeq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("EDASeq")
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 2.2.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
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)
LinkingTo
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth
SystemRequirements
Enhances
URL
Depends On Me metaseqR, RUVSeq
Imports Me EnrichmentBrowser
Suggests Me HTSFilter, oneChannelGUI
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source EDASeq_2.2.0.tar.gz
Windows Binary EDASeq_2.2.0.zip
Mac OS X 10.6 (Snow Leopard) EDASeq_2.2.0.tgz
Mac OS X 10.9 (Mavericks) EDASeq_2.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/EDASeq/tree/release-3.1
Package Short Url http://bioconductor.org/packages/EDASeq/
Package Downloads Report Download Stats

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