ArticleHuman genomics2024
Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses.
Article in Human genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.Cell reports methods · 2026Article
- Differential expression analysis in single cell and spatial RNASeq without model assumptions.bioRxiv : the preprint server for biology · 2025Article
- Modeling tumor dynamics and predicting response to therapies in a murine pancreatic cancer model.NPJ systems biology and applications · 2025Article
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7 authors.
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Abstract
backgroundSingle 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.
resultsMotivated 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.
conclusionIn 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.
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