Systematic analysis of alternative splicing in time course data using Spycone

Motivation: During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. Results: Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection.