Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of RNA-seq quantification using the Salmon software package. The entire pipeline is fast, benefiting from inference steps by Salmon to quantify expression at the transcript level. The

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... orkflow includes live, runnable code chunks for analysis using DRIMSeq and DEXSeq, as well as for performing two-stage testing of DTU using the stageR package, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU. We evaluate these packages and other related packages on a simulated dataset with parameters estimated from real data.