Table 1.
Qualitative comparison of signature scoring methods based on their properties, influencing factors, and score comparability
| Scoring method | Deterministic | Optimal control gene selection | Independent of total cell number and cell-type proportions | Robust to batch effect when scoring all samples together | Robust when scoring for small signatures | Robust to unrelated genes in the signature | Provides comparable scores for multiple cell-type signatures |
|---|---|---|---|---|---|---|---|
| Adjusted Neighborhood Scoring (ANS) | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ |
| SCANPY (Wolf et al. 2018): based on work by Tirosh et al. (2016) | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Seurat (Satija et al. 2015): based on work by Tirosh et al. (2016) | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Seurat_AG | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Seurat_LVG | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
| Jasmine_LH (Noureen et al. 2022) | ✓ | NA | ✗ | ✓ | ✓ | ✓ | ✗ |
| Jasmine_OR (Noureen et al. 2022) | ✓ | NA | ✗ | ✓ | ✗ | ✓ | ✗ |
| UCell (Andreatta and Carmona 2021) | ✓ | NA | ✓ | ✓ | ✓ | ✓ | ✗ |
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A check mark indicates a scoring method fulfills property or resists an influencing factor; a cross mark, the opposite. (Seurat_AG) Seurat scoring with all genes as control; (Seurat_LVG) Seurat scoring with least variable genes as control; (Jasmine_LH) JASMINE with likelihood computation; (Jasmine_OR) JASMINE with odds-ratio computation; (NA) a property or an influencing factor that cannot be evaluated for a scoring method. These results are discussed in detail in the Results section.
