DOI: 10.18129/B9.bioc.DEXSeq  

This is the development version of DEXSeq; for the stable release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel


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


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biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.47.0
In Bioconductor since BioC 2.9 (R-2.14) (11.5 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
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2
Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU
Imports Me diffUTR, IntEREst, pairedGSEA
Suggests Me bambu, BioPlex, GenomicRanges, satuRn, stageR, subSeq
Links To Me
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