Table 1.
Description of scRNA-seq datasets
| Dataset name | Size (cells × genes) | Number of clusters | Cluster sizes | |
|---|---|---|---|---|
| 1 | Quake Smart seq2 Trachea | 1350 × 23,341 | 4 | (830, 206, 201, 113) |
| 2 | Quake10 × Bladder | 2500 × 23,341 | 4 | (1203, 1167, 73, 57) |
| 3 | Quake10 × Spleen | 9552 × 23,341 | 5 | (6886, 1930, 464, 230, 42) |
| 4 | Quake Smart seq2 Diaphragm | 870 × 23,341 | 5 | (439, 241, 81, 78, 31) |
| 5 | Quake10 × Limb Muscle | 3909 × 23,341 | 6 | (1330, 1136, 461, 354, 320, 308) |
| 6 | Quake Smart seq2 Limb Muscle | 1090 × 23,341 | 6 | (540, 258, 141, 71, 45, 35) |
| 7 | Romanov | 2881 × 21,143 | 7 | (1001, 898, 356, 267, 240, 71, 48) |
| 8 | Adam | 3660 × 23,797 | 8 | (629, 617, 516, 513, 463, 396, 302, 224) |
| 9 | Muraro | 2122 × 19,046 | 9 | (812, 448, 245, 219, 193, 101, 80, 21, 3) |
| 10 | Young | 5685 × 33,658 | 11 | (1498, 1201, 731, 621, 483, 373, 268, 259, 118, 73, 60) |
| 11 | Quake Smart seq2 Lung | 1676 × 23,341 | 11 | (693, 423, 113, 90, 85, 65, 57, 53, 37, 35, 25) |
| 12 | 10 PBMC | 4271 × 16,653 | 8 | (1292, 702, 606, 459, 450, 332, 295, 135) |
| 13 | Mouse ES cells | 2717 × 24,175 | 4 | (933, 798, 683, 303) |
| 14 | Worm neuron cell | 4186 × 13,488 | 10 | (1015, 842, 443, 400, 334, 314, 305, 239, 224, 70) |
| 15 | Mouse bladder cell | 2746 × 20,670 | 16 | (717, 357, 344, 316, 236, 224, 131, 80, 75, 64, 44, 41, 38, 36, 30, 13) |
The datasets made available in scziDesk have been combined with those in scDeepClusters to create a wider benchmark of 15 datasets