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

DEXSeq

Inference of differential exon usage in RNA-Seq

Bioconductor version: 2.13

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Author: Simon Anders <sanders at fs.tum.de> and Alejandro Reyes <alejandro.reyes at embl.de>, both at EMBL Heidelberg

Maintainer: Alejandro Reyes <alejandro.reyes at embl.de>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("DEXSeq")

 

PDF	R Script	Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, HighThroughputSequencing, RNAseq, Software
Version	1.8.0
In Bioconductor since	BioC 2.9 (R-2.14)
License	GPL (>= 3)
Depends	Biobase(>= 2.13.11)
Imports	BiocGenerics(>= 0.7.5), biomaRt, hwriter, methods, stringr, GenomicRanges, Rsamtools, statmod (>= 1.4.15)
Suggests	GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.13), parathyroidSE, BiocStyle
System Requirements
URL
Depends On Me	parathyroid
Imports Me
Suggests Me	GenomicRanges, oneChannelGUI, pasilla

Package Archives

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

Package Source	DEXSeq_1.8.0.tar.gz
Windows Binary	DEXSeq_1.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	DEXSeq_1.8.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats