Fig. 1

Schematic illustration of our cell-type assignment approach. It consists of five steps: (1) generating synthetic single-cell read counts (gray rectangles) for the CDSeq-estimated cell-type-specific GEPs (white rectangles); (2) combining the pseudo scRNA-seq data with user-provided scRNA-seq data (colored rectangles), then performing clustering using Seurat; (3) visualizing the result using tSNE plot to show the 2D embedding of the clustering outcomes with differently colored circles denoting distinctive cell types in the single-cell data and gray squares denoting the CDSeq-identified cell types; (4) annotating each cluster to the cell type to which the majority of the cells in the cluster belong; (5) assigning the CDSeq-identified cell types accordingly as in step 4