ScIsoX: A Multidimensional Framework for Measuring Isoform-Level Transcriptomic Complexity in Single Cells

Single-cell isoform sequencing enables high-resolution characterisation of transcript isoform expression, yet analytical frameworks to systematically measure transcriptomic complexity are lacking. Here, we introduce ScIsoX , a computational framework that integrates a novel hierarchical data structure, a suite of complexity metrics, and dedicated visualisation tools for isoform-level analysis. ScIsoX supports systematic exploration of global and cell-type-specific isoform expression patterns arising from alternative splicing, revealing multidimensional complexity signatures across diverse datasets - insights often missed by conventional gene-level approaches.