AS (alternative splicing) is a common mechanism of post-transcriptional gene regulation in eukaryotic organisms that expands the functional and regulatory diversity of a single gene by generating multiple mRNA isoforms that encode structurally and functionally distinct proteins. ASpli is an integrative pipeline and user-friendly R package that facilitates the analysis of changes in both annotated and novel AS events. ASpli integrates several independent signals in order to deal with the complexity that might arise in splicing patterns.