From: Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Method | Mean AMI | Mean silhouette | ||||||
---|---|---|---|---|---|---|---|---|
Default | Best | ANOVA AMI heuristic | Silhouette heuristic | Default | Best | ANOVA AMI heuristic | Silhouette heuristic | |
scran | 0.840 | 0.868 | 0.841 | 0.741 | 0.362 | 0.547 | 0.396 | 0.494 |
Seurat | 0.788 | 0.860 | 0.814 | 0.683 | 0.369 | 0.543 | 0.490 | 0.373 |
ZinbWave | 0.780 | 0.896 | 0.851 | 0.825 | 0.249 | 0.609 | 0.562 | 0.591 |
DCA | 0.758 | 0.885 | 0.837 | 0.583 | 0.396 | 0.639 | 0.403 | 0.381 |
scVI | 0.560 | 0.872 | 0.709 | 0.510 | 0.384 | 0.621 | 0.482 | 0.318 |