Fig. 3
From: CoCoA-diff: counterfactual inference for single-cell gene expression analysis
The case study of Alzheimer’s disease snRNA-seq profiles [22]. Cell-type-stratified approach improves statistical power and interpretation of differential expression analysis. a UMAP projection of the major cell types. b UMAP projection of the excitatory neuron subtypes. c UMAP projection of the inhibitory neuron subtypes. d Cell type decomposition of the major cell types across 48 individuals. e Cell type decomposition of the excitatory neurons across 48 individuals. f Cell type decomposition of the inhibitory neurons across 48 individuals. g, h Cell-type-stratified CoCoA-diff approach improves statistical power and identifies genes in a wide spectrum of the cell types. i A genomic view of genes strongly modulated by AD pathology (coloured). Top panel: genomic location of cell-type-specific causal genes; bottom panels: five representative examples of the most significant genes