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Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses

Authors :
Gang Han
Dongyan Yan
Zhe Sun
Jiyuan Fang
Xinyue Chang
Lucas Wilson
Yushi Liu
Source :
Human Genomics, Vol 18, Iss 1, Pp 1-13 (2024)
Publication Year :
2024
Publisher :
BMC, 2024.

Abstract

Abstract Background Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. Results Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study. Conclusion In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.

Details

Language :
English
ISSN :
14797364
Volume :
18
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Human Genomics
Publication Type :
Academic Journal
Accession number :
edsdoj.07d6b62480f74e9abb8ace35007dc747
Document Type :
article
Full Text :
https://doi.org/10.1186/s40246-024-00638-0