DEXSeq

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq


Bioconductor version: 3.17

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.ds at gmail.com>

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

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DEXSeq")

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

Documentation

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

browseVignettes("DEXSeq")
Inferring differential exon usage in RNA-Seq data with the DEXSeq package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version 1.46.0
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
URL
See More
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2
Linking To
Enhances
Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU
Imports Me diffUTR, IntEREst, pairedGSEA
Suggests Me bambu, BioPlex, GenomicRanges, satuRn, stageR, subSeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package DEXSeq_1.46.0.tar.gz
Windows Binary DEXSeq_1.46.1.zip
macOS Binary (x86_64) DEXSeq_1.46.1.tgz
macOS Binary (arm64) DEXSeq_1.46.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEXSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEXSeq
Bioc Package Browser https://code.bioconductor.org/browse/DEXSeq/
Package Short Url https://bioconductor.org/packages/DEXSeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive