MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data

Wei Xiong Wen; Adam J Mead; Supat Thongjuea

doi:10.1093/nar/gkac1260

MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data

Nucleic Acids Res. 2023 Mar 21;51(5):e29. doi: 10.1093/nar/gkac1260.

Authors

Wei Xiong Wen^{1

2}, Adam J Mead^{1

3}, Supat Thongjuea^{1

2

3}

Affiliations

¹ MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
² MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
³ NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK.

Abstract

Alternative splicing is an important source of heterogeneity underlying gene expression between individual cells but remains an understudied area due to the paucity of computational tools to analyze splicing dynamics at single-cell resolution. Here, we present MARVEL, a comprehensive R package for single-cell splicing analysis applicable to RNA sequencing generated from the plate- and droplet-based methods. We performed extensive benchmarking of MARVEL against available tools and demonstrated its utility by analyzing multiple publicly available datasets in diverse cell types, including in disease. MARVEL enables systematic and integrated splicing and gene expression analysis of single cells to characterize the splicing landscape and reveal biological insights.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing*
Computational Biology
RNA Splicing
Sequence Analysis, RNA
Single-Cell Analysis
Software*