DEXSeq

DOI: 10.18129/B9.bioc.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>

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")

 

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

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 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
LinkingTo
Suggests	GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2
SystemRequirements
Enhances
URL
Depends On Me	IsoformSwitchAnalyzeR, pasilla, rnaseqDTU
Imports Me	diffUTR, IntEREst, pairedGSEA
Suggests Me	bambu, BioPlex, GenomicRanges, satuRn, stageR, subSeq
Links To Me
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