DOI: 10.18129/B9.bioc.DEXSeq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq

Bioconductor version: 3.16

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")):


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biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.44.0
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(>= 1.9.11), 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
Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU
Imports Me diffUTR, IntEREst
Suggests Me bambu, BioPlex, GenomicRanges, satuRn, stageR, subSeq
Links To Me
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Source Package DEXSeq_1.44.0.tar.gz
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