DEXSeq

Version:

1.4

Category:

bio

Cluster:

Loki

Author / Distributor

https://https://www.bioconductor.org/

Description

DEXSeq is a Bioconductor package for differential exon usage analysis in RNA-Seq datasets. It allows researchers to detect changes in exon usage that may result from alternative splicing events, even in the absence of differential gene expression.

Key features:

  • Exon-level statistical modeling using generalized linear models

  • Supports visualization of exon usage and normalized counts

  • Works with standard alignment outputs (BAM/GTF)

  • Compatible with workflows using HTSeq and DESeq2

DEXSeq is particularly useful for studying transcriptome complexity and alternative splicing across experimental conditions.

Documentation

DEXSeq is an R/Bioconductor package and is used within the R environment.

To load DEXSeq in R:

    library(DEXSeq)

To see help:

    ?DEXSeq
    browseVignettes("DEXSeq")

Example command:

    dxd <- DEXSeqDataSetFromHTSeq(countFiles, design, flattenedFile)
    dxd <- estimateSizeFactors(dxd)
    dxd <- estimateDispersions(dxd)
    dxd <- testForDEU(dxd)
    dxd <- estimateExonFoldChanges(dxd, fitExpToVar="condition")
    results <- DEXSeqResults(dxd)

Official vignette:
  https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html

Examples/Usage

  • Load the DEXSeq module:

$ module load bio/dexseq/1.40

  • Start an R session and load the package:

library(DEXSeq)

  • Access the DEXSeq vignette:

browseVignettes("DEXSeq")

  • Typical workflow (in R):

dxd <- DEXSeqDataSetFromHTSeq(countFiles, sampleData, design= ~ sample + exon + condition:exon)
dxd <- estimateSizeFactors(dxd)
dxd <- estimateDispersions(dxd)
dxd <- testForDEU(dxd)
dxd <- estimateExonFoldChanges(dxd, fitExpToVar="condition")
results <- DEXSeqResults(dxd)

  • Unload the module:

$ module unload bio/dexseq/1.40

Installation

https://bioconductor.org/packages/DEXSeq/