DOI: 10.18129/B9.bioc.DEXSeq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq

Bioconductor version: 3.8

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> and Alejandro Reyes <alejandro.reyes.ds at>

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

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


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



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


biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.28.3
In Bioconductor since BioC 2.9 (R-2.14) (7.5 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
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr
Depends On Me IsoformSwitchAnalyzeR, rnaseqDTU
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_1.28.3.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) DEXSeq_1.28.3.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: