Table 1.
Major characteristics of the 12 benchmarking datasets
| #Estimated clusters |
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Organism | #Single cells | #True clusters | SC3 | CIDR | Seurat | t-SNE + k-means | SAFE-clustering | Ref | |
| Baron_human1 | Human | 1937 | 14 | 23 | 3 | 12 | 11 | 11 | Baron et al., 2016 |
| Baron_human2 | Human | 1724 | 14 | 23 | 9 | 10 | 6 | 5 | Baron et al., 2016 |
| Baron_human3 | Human | 3605 | 14 | 37 | 5 | 12 | 7 | 14 | Baron et al., 2016 |
| Baron_human4 | Human | 1303 | 14 | 19 | 3 | 9 | 4 | 8 | Baron et al., 2016 |
| Baron_mouse1 | Mouse | 822 | 13 | 18 | 13 | 9 | 9 | 9 | Baron et al., 2016 |
| Biase | Mouse | 49 | 3 | 3 | 5 | 3 | 3 | 4 | Biase et al., 2014 |
| Darmanis | Human | 420 | 8 | 11 | 7 | 5 | 5 | 5 | Darmanis et al., 2015 |
| Ting | Mouse | 187 | 7 | 13 | 10 | 5 | 6 | 9 | Ting et al., 2014 |
| Yan | Human | 90 | 7 | 5 | 5 | 3 | 3 | 3 | Yan et al., 2013 |
| Zeisel | Mouse | 3005 | 9 | 32 | 5 | 13 | 6 | 13 | Zeisel et al., 2015 |
| simple case PBMC mixture | Human | 28 733 | 3 | 3 | 3 | 16 | 4 | 3 | Zheng et al., 2017 |
| challenging case PBMC mixture | Human | 32 695 | 3 | 2 | 10 | 14 | 3 | 3 | Zheng et al., 2017 |
Note. The characteristics include organism origin, number of single cells, the numbers of true and estimated clusters by SAFE-clustering and four individual methods, as well as references.