Dynast: Inclusive and efficient quantification of metabolically labeled transcripts in single cells

Abstract

Single cell RNA velocity, defined as the time derivative of gene expression, is a powerful concept that can predict the future transcriptional state of the cell. Traditionally, RNA velocity estimations relied on the distinction between spliced and unspliced mRNA in single cell RNA-seq (scRNA-seq) data, resulting in noisy and biased approximations. Recent advancements in metabolic labeling enabled the direct, unbiased measurement of nascent RNA, yielding significantly improved RNA velocity estimates. However, there is still a lack of a standardized computational framework to process these data. This study introduces Dynast, a pipeline to comprehensively and efficiently quantify metabolically labeled and splicing transcripts from high-throughput metabolic labeling-enabled scRNA-seq.