DEXSeq

Inference of differential exon usage in RNA-Seq

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

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

    citation("DEXSeq")

Documentation

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

Details

biocViews DifferentialExpression, RNASeq, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 2.9 (R-2.14)
License GPL (>= 3)
Depends Biobase, GenomicRanges, IRanges, DESeq2(>= 1.3.69), BiocParallel
Imports BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr
System Requirements
URL
Depends On Me parathyroid
Imports Me
Suggests Me GenomicRanges, oneChannelGUI, pasilla

Package Downloads

Package Source DEXSeq_1.10.0.tar.gz
Windows Binary DEXSeq_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DEXSeq_1.10.0.tgz
Mac OS X 10.9 (Mavericks)
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