Fig. 1

The SuperCellCyto framework. A Schematic overview of the SuperCellCyto R package for generating supercells from cytometry data. B Proposed workflow for an end-to-end cytometry data analysis using supercells as the fundamental unit of analysis. The workflow begins with the generation of supercells using SuperCellCyto from cleaned and transformed cytometry data. If necessary, batch correction is then performed at the supercell level. Supercells are then clustered and annotated based on the cell type they represent. Differential expression analysis can be performed using existing tools such as Limma following aggregation of supercells at the sample and cell type level. Differential abundance analysis is performed after expanding supercells back to single cells using existing tools such as Propeller