Using ANCOMBC for single-cell RNAseq data

[JB3122]

While reading the recent publication by Macnair et al. on snRNA-seq in multiple sclerosis (10.1016/j.neuron.2024.11.016), I wanted to explore ANCOMBC for single-cell RNA-seq analysis. Specifically, I have identified various T-cell states from scRNA-seq data and would like to assess differential abundance of these states across different anatomical locations.

Although ANCOMBC was originally designed for microbiome abundance analysis, its underlying principles, such as the interdependence between different taxa and the ability to account for varying sample sizes, seem well-suited for single-cell data. In my study, accounting for covariates like age, BMI, and smoking status is also essential, as these factors are known to influence T-cell composition in humans.

Does anyone have any experience doing this ? If so, any tips would be greatly appreciated.