Fig. 3

ddqc retains biologically meaningful cells that conventional QC filters out. A Overview of the ddqc approach. B, C ddqc retains more cells when compared to the standard cutoff approach across B tissues in the Tabula Muris dataset, and C scRNA-seq data generating technologies. D UMAP visualization of Tabula Muris lung cells. Colors represent whether the cells are included in the paper or uniquely retained by ddqc. E Violin plot visualization of cell type-specific signature scores in average log(TPX+1). From top to bottom: muscle, neutrophil, NK cells, and Gamma-delta T cells. F UMAP visualization of joint clustering of cells retained by both ddqc and the standard cutoff in the Tabula Muris heart and aorta tissues. G Proportion of cells retained by ddqc, standard cutoff, or both in the mouse heart and aorta tissues