Differential Expression vs. Differential Transcript Usage: Sleuth and DRIMSeq

Sai Indu Alekhya Lingala

Abstract: This paper provides a comparative evaluation of two computational tools-Sleuth and DRIMSeq-for analyzing single-cell RNA sequencing data at the transcript level. Sleuth focuses on identifying differential expression in transcript abundance, integrating quantification uncertainty through bootstrapping methods. In contrast, DRIMSeq targets differential transcript usage by modeling isoform proportions using a Dirichlet-multinomial framework. The review outlines the statistical foundations, application contexts, and practical limitations of each tool, emphasizing their suitability for different research questions. By clarifying when and why to use each approach, this article supports informed decision-making in transcriptomic studies.

Keywords: Single-cell RNA-seq, Sleuth, DRIMSeq, transcript analysis, differential expression

How to Cite?: Sai Indu Alekhya Lingala, "Differential Expression vs. Differential Transcript Usage: Sleuth and DRIMSeq", Volume 14 Issue 10, October 2025, International Journal of Science and Research (IJSR), Pages: 11-15, https://www.ijsr.net/getabstract.php?paperid=SR25929103524, DOI: https://dx.doi.org/10.21275/SR25929103524