Table 2.

Parameters and their ranges for simulating the UMI and nonUMI databases

Parameters	non-UMI database	UMI database
Sigma (σ): within-population heterogeneity	0.1, 0.2, 0.6	0.2, 0.6
Gene_effects_sd: standard deviation for generating gene effect vectors	1, 2	2
scale_s: cell size parameter, use small values for cell types known to be small	0.3, 0.5, 0.6, 1	0.1, 0.2, 0.3, 0.4, 0.5, 0.7, 1
prop_hge: proportion of extreme high-expression outlier genes	0.015, 0.02, 0.025, 0.03	0.01, 0.015, 0.02, 0.025, 0.03
mean_hge: scale factor for high-expression outlier genes	3, 4, 5, 6	3, 4, 5, 6
Alpha_mean (α): mean mRNA capture efficiency	0.05, 0.1, 0.15, 0.2, 0.25	0.007, 0.01, 0.02, 0.03, 0.04, 0.05, 0.07, 0.1
Alpha_sd (β): standard deviation of mRNA capture efficiency across cells	0.005, 0.01, 0.015, 0.02, 0.03, 0.045, 0.06, 0.075	7e-04, 0.001, 0.0014, 0.002, 0.003, 0.0035, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.012, 0.015, 0.02, 0.025, 0.03, 0.035, 0.05
depth_mean (depth): mean sequencing depth for a set of cells	1e + 05, 5e + 05, 1e + 06, 2e + 06	45,000, 70,000, 95,000, 150,000, 3e + 05, 5e + 05
Depth_sd: standard deviation of sequencing depth for a set of cells	100,00,30,000, 50,000, 1e + 05, 150,000, 2e + 05, 3e + 05, 6e + 05	4500, 7e3, 9e3, 9.5e3, 13500, 14e3, 15e3, 19e3, 21e3, 22,500, 28,500, 3e4, 35e3, 4.5e4, 47500, 5e4, 7.5e4, 9e4, 15e4, 25e4
nPCR1: number of PCRs in pre-amplification phase	14, 18	10, 14