Hypatia: a statistical framework for single-cell RNA isoform data analysis

Long-read single-cell RNA-sequencing (LR-scRNAseq) enables isoform quantification at single-cell resolution. However, methods to assess isoform complexity between cell populations are lacking.

To address this, we present Hypatia, a toolkit for analyzing isoform usage shifts, diversity, and expression. Using simulated data, we establish a framework for comparative analysis. Using three LR-scRNAseq data sets, we identify widespread transcript-level heterogeneities across cells.