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.
Availability and Implementation: The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2022. Published by Oxford University Press.)