DEXSeq

DOI: 10.18129/B9.bioc.DEXSeq    

Inference of differential exon usage in RNA-Seq

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DEXSeq", version = "3.8")

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")

 

PDF R Script Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Visualization
Version 1.28.0
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License GPL (>= 3)
Depends BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors
Imports BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
LinkingTo
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me IsoformSwitchAnalyzeR, rnaseqDTU
Imports Me IntEREst
Suggests Me GenomicRanges, JctSeqData, pasilla, stageR, subSeq
Links To Me
Build Report  

Package Archives

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

Source Package DEXSeq_1.28.0.tar.gz
Windows Binary DEXSeq_1.28.0.zip
Mac OS X 10.11 (El Capitan) DEXSeq_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEXSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEXSeq
Package Short Url http://bioconductor.org/packages/DEXSeq/
Package Downloads Report Download Stats

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