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Table 4 Clustering evaluation results. The NMI, AMI, and ARI scores are the cell type clustering results using SnapATAC software. “Real-input data” refers to the clustering results using the input real scATAC-seq data. Metrics for simATAC’s simulated bin-by-cell matrices for different noise levels are also compared presented for each of the Buenrostro2018, Cusanovich2018, and PBMCs datasets

From: simATAC: a single-cell ATAC-seq simulation framework

Mean Standard deviation NMI AMI ARI
Buenrostro2018
0 0 0.71 0.83 0.54
− 0.3 0.3 0.72 0.83 0.54
− 0.4 0.4 0.67 0.78 0.50
Real-input data   0.54 0.62 0.36
Cusanovich2018
0 0 0.96 0.97 0.94
− 0.3 0.3 0.79 0.85 0.69
− 0.4 0.4 0.62 0.71 0.40
Real-input data   0.41 0.46 0.22
PBMCs
0 0 0.78 0.87 0.71
− 0.3 0.3 0.61 0.73 0.47
− 0.4 0.4 0.56 0.67 0.44
Real-input data   0.45 0.54 0.28