Alternative splicing represents an additional and under-appreciated layer of complexity underlying gene expression profiles. More recently, technological advances in library preparation methodologies enabled capturing and amplification of full-length cDNAs from single cells. Thus, paving the way for splicing analysis at single-cell resolution.
Nevertheless, single-cell splicing analysis comes with its own set of challenges including, but not limited to, low coverage of lowly-expressed genes, low capture rate of cDNA molecules, and amplification bias (Wen et al., 2020). To date, there remains a paucity of peer-reviewed softwares available for single-cell splicing analysis. Notable examples are BRIE (Huang & Sanguinetti, 2017) and Expedition (Song et al., 2017).
Here, we introduce MARVEL (Multimodal Approach to ReVEaL alternative splicing dynamics at single-cell resolution). MARVEL includes features that complement existing softwares in order to more comprehensively describe and reveal splicing dynamics at single-cell resolution.
Tutorials for both plate- and droplet-based alternative splicing analysis using MARVEL can be found here: https://github.com/wenweixiong/MARVEL