Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis

Table 1 Benchmark datasets

Dataset	Technology	Organism	N cells	Cell types	N types	Ref.
Zhengmix4eq	10x	Human	3,909	B (24.5%), Monocytes (24.5%), cytoT (25.5%), rT (25.5%)	4	[11, 21]
Zhengmix4uneq	10x	Human	6,345	B (15%), Monocytes (30%), cytoT (8%), rT (46%)	4	[11, 21]
Zhengmix5eq	10x	Human	4,876	hT (20%), mT (20%), cytoT (20%), nT (20%), rT (20%)	5	[21]
Zhengmix8eq	10x	Human	3,908	B (12.5%), Monocytes (14.5%), hT (10%), NK (15%), mT (12.5%), cytoT (10%), nT (13%), rT (12.5%)	8	[11, 21]
Zhengmix8uneq	10x	Human	6,350	B (7.5%), Monocytes (15%), hT (8%), NK (4%), mT (15%), cytoT (4%), nT (23%), rT	8	[21]
sc_10x	10x	Human	902	H1975 (34.5%), H2228 (35%), HCC827 (30.5%)	3	[12]
sc_10x_5cl	10x	Human	3,918	A549 (32%), H1975 (11%), H2228 (19.5%), H838 (22.5%), HCC827 (15%)	5	[12]
sc_celseq2	CEL-Seq2	Human	274	H1975 (41%), H2228 (29.5%), HCC827 (29.5%)	3	[12]
sc_celseq2_5cl	CEL-Seq2	Human	895	A549 (36%), H1975 (14.5%), H2228 (14%), H838 (22%), HCC827 (13.5%)	5	[12]
TabulaMuris	Smart-Seq2	Murine	12,081	Brain (36.5%), intestine (31.5%), skin (19%), spleen (13%)	4	[22]

The first five datasets are derived from [21] and [11] and contain CD19+ B cells (B), CD14+ monocytes (Monocytes), CD4+ helper T cells (hT), CD56+ natural killer cells (NK), CD4+/CD45RO+ memory T cells (mT), CD8+/CD45RA+ naive cytotoxic T cells (cytoT), CD4+/CD45RA+/CD25 − naive T cells (nT), and CD4+/CD25+ regulatory T cells (rT). The four next are from [12] and contain the five following cell lines: A549, H1975, H2228, H838, and HCC827. The last one is from [22]

ISSN: 1474-760X