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Inference of differential exon usage in RNA-Seq

Bioconductor version: Release (3.19)

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 "4.4") and enter:

if (!require("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:

Inferring differential exon usage in RNA-Seq data with the DEXSeq package HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>= 3)
Depends BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors(>= 0.23.18)
Imports BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
System Requirements
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Suggests GenomicFeatures, txdbmaker, pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi
Linking To
Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU
Imports Me diffUTR, IntEREst, pairedGSEA, saseR
Suggests Me bambu, GenomicRanges, satuRn, stageR, subSeq, BioPlex
Links To Me
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Package Archives

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

Source Package DEXSeq_1.50.0.tar.gz
Windows Binary
macOS Binary (x86_64) DEXSeq_1.50.0.tgz
macOS Binary (arm64) DEXSeq_1.50.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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