DEXSeq

DOI: 10.18129/B9.bioc.DEXSeq    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq

Bioconductor version: 3.7

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.ds at gmail.com>

Maintainer: Alejandro Reyes <alejandro.reyes.ds at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Visualization
Version	1.26.0
In Bioconductor since	BioC 2.9 (R-2.14) (7 years)
License	GPL (>= 3)
Depends	BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors
Imports	BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
LinkingTo
Suggests	GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	IntEREst
Suggests Me	GenomicRanges, JctSeqData, pasilla, stageR, subSeq
Links To Me
Build Report

Package Archives

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

Source Package	DEXSeq_1.26.0.tar.gz
Windows Binary	DEXSeq_1.26.0.zip
Mac OS X 10.11 (El Capitan)	DEXSeq_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEXSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEXSeq
Package Short Url	http://bioconductor.org/packages/DEXSeq/
Package Downloads Report	Download Stats