Table 1.

The scRNA-seq datasets used for comparing the performance of different tools

Dataset	k	# cells	Standard	Cell Label Definition	UMI	Ref
Pollen	11	301	gold	human cell lines	No	[8]
Deng	10	286	bronze	Stages of mouse preimplantation development	No	[6]
Usoskin	4	622	silver	Clusters of mouse lumbar DRG (dorsal root ganglion)	No	[35]
Blakeley	3	30	gold	Human pluripotent epiblast cells, extraembryonic trophectoderm cells and primitive endoderm cells	No	[32]
Treutlein	8	405	bronze	Cell populations from direct reprogramming from fibroblast to neuron (MEF, day 2, 5, and 22)	No	[36]
Zheng	10	94,655	gold	Cell populations from human immune system	Yes	[33]
Hrvatin	8	48,266	silver	Cell populations from mouse visual cortex	Yes	[34]
Scialdone	4	1205	bronze	Stages of mouse mesodermal development	No	[37]
Petropoulos	5	1529	bronze	Stages of human preimplantation development	No	[38]

k represents the number of cell clusters reported in the original study. Datasets were grouped into three levels (gold, silver and bronze standards) based on the supporting evidence of the reported cell labels