Streamlining differential exon and 3′ UTR usage with diffUTR

BACKGROUND: Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data. RESULTS: We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3′ UTR usage analysis. We demonstrate the diffUTR features and show that it is more flexible and more accurate than state-of-the-art alternatives, both in simulations and in real data. CONCLUSIONS: diffUTR enables differential 3′ UTR analysis and more generally facilitates DEU and the exploration of their results. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04114-7.