DEXSeq

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.

Inference of differential exon usage in RNA-Seq

Bioconductor version: 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 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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization

Version 1.50.0

In Bioconductor since BioC 2.9 (R-2.14) (13 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

Suggests GenomicFeatures, txdbmaker, pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi

Linking To

Enhances

Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU

Imports Me IntEREst, diffUTR, pairedGSEA, saseR

Suggests Me GenomicRanges, bambu, satuRn, stageR, subSeq, BioPlex

Links To Me

Build Report Build Report

Package Archives

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

Source Package DEXSeq_1.50.0.tar.gz

Windows Binary (x86_64) DEXSeq_1.50.0.zip (64-bit only)

macOS Binary (x86_64) DEXSeq_1.50.0.tgz

macOS Binary (arm64) DEXSeq_1.50.0.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