Table 3.
Time (in s) and memory (in MiB) for execution of Scanpy, SC3 and Seurat methods in several single cell banks
| Method | ||||||||
|---|---|---|---|---|---|---|---|---|
| Data | Number of | Number of | Scanpy | SC3 | Seurat | |||
| set | cells | genes | Time | Memory | Time | Memory | Time | Memory |
| Wang | 71,032 | 100 | 81.97 | 9194.92 | (1) | 123.75 | 483.89 | |
| 500 | 100.69 | 9541.20 | (1) | 151.63 | 1238.48 | |||
| 4000 | 229.94 | 11786.49 | 2907.28 | 8334.96 | 299.47 | 5828.26 | ||
| all | 178.63 | 11572.80 | 6202.98 | 40560.79 | 717.55 | 27332.94 | ||
| Garcia | 100,307 | 100 | 117.89 | 13616.54 | (1) | 202.43 | 476.88 | |
| 500 | 142.09 | 14174.46 | (1) | 204.96 | 940.13 | |||
| 4000 | 338.65 | 17515.35 | 3047.56 | 8411.55 | 347.43 | 5397.71 | ||
| all | 340.17 | 12055.15 | 6050.07 | 51085.32 | 1198.42 | 32640.66 | ||
| Fonseca | 118,144 | 100 | 120.84 | 8014.76 | (1) | 191.96 | 448.31 | |
| 500 | 159.91 | 8944.68 | (1) | 252.76 | 1002.43 | |||
| 4000 | 388.47 | 12011.64 | 2606.85 | 9017.33 | 415.30 | 4996.09 | ||
| all | 178.63 | 11572.80 | 4752.91 | 73529.04 | 1678.49 | 31231.88 | ||
| Merge | 289,483 | 100 | 638.00 | 30738.78 | (1) | 631.02 | 950.68 | |
| 500 | 490.14 | 32033.64 | (1) | 706.44 | 2266.57 | |||
| 4000 | 1111.51 | 40586.07 | 2960.67 | 21616.60 | 1017.365 | 13205.54 | ||
| all | 1454.21 | 41961.79 | (2) | (2) | ||||
SC3 was applied with 64 threads; Scanpy and Seurat do not allow the number of threads to be chosen
(1): Application of SC3 with 100 and 500 genes caused a program error
(2): Program crashes without error messages due to memory exhaustion on a 256 GiB machine