Extended Data Fig. 4: Validation and performance evaluation of scDeepLUCIA for scHiCAR loop calling.
a. Relative number of loops identified by the indicated loop callers from GM12878 scHiCAR dataset (148M) before and after 10k cell downsampling (15M). b. Number of loops identified by scDeepLUCIA and Peakachu across 22 mouse brain cell clusters, ordered by the number of captured cells in each cluster. c. Receiver operating characteristic (ROC) curve and AUROC of the scDeepLUCIA model trained on the loops from downsampled astrocyte bulk HiCAR. d. Number of loops identified by scDeepLUCIA and Peakachu in downsampled L23IT-1 cell cluster. e-f. Chromatin contact maps and identified loops before and after downsampling in oligodendrocyte (e) and Pvalb (f). g. Loop recovery rate after downsampling relative to the number of loops identified in the full dataset (120,000 cells). h. Aggregate peak analysis (APA) plot of cell type specific loops identified by scDeepLUCIA. Loop anchors are centered, with ±20 neighboring bins (5kb resolution) shown. i. Genome browser snapshots displaying scDeepLUCIA loops, open chromatin peaks, compartment A/B, and gene expression for cell type specific marker gene, Car2 in oligodendrocyte (Oligo).
