EDASeq

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: 2.10

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, HighThroughputSequencing, Preprocessing, QualityControl, RNAseq, Software
Depends	BiocGenerics(>= 0.1.3), Biobase(>= 2.15.1), ShortRead(>= 1.11.42), Rsamtools(>= 1.5.75), aroma.light
Imports	methods, graphics, BiocGenerics, IRanges(>= 1.13.9), DESeq
Suggests	yeastRNASeq, leeBamViews, edgeR, DESeq
System Requirements
License	Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me	oneChannelGUI
Version	1.2.0
Since	Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source	EDASeq_1.2.0.tar.gz
Windows Binary	EDASeq_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	EDASeq_1.2.0.tgz
Package Downloads Report	Download Stats

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