Table 1.
Feature comparison of CellCall with other tools
| CellCall | CellPhoneDB | SingleCellSignalR | CellChat | Nichenet | NATMI | iTALK | RNA-Magnet | SoptSC | ICELLNET | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Data | Data size | 19 144 (L–R–TF) | 1396 | 3251 | 1939 | 12 019 | 2187 | 2649 | 2000 | N | 380 |
| Literature supported L–R interactions | 1141 | 398 | 1483 | 891 | 0 | 2187 | 0 | 1618 | N | 379 | |
| Intracellular signaling | KEGG | N | KEGG/ Reactome | N | multiple sources | N | N | N | N | N | |
| Complex | Y | Y | N | Y | N | N | N | N | N | Y | |
| Approach | Scoring based on expression | L/R/TG | L/R | L/R | L/R | L/R/TG | L/R | L/R | L/R | L/R/ Downstream gene | L/R |
| Score threshold | TF activities | Permutation test | ad hoc benchmark | Permutation test | N | N | Differentially expressed | N | N | N | |
| Pathway activity analysis | Y | N | N | N | N | N | N | N | N | N | |
| Visualization | Heatmap | Y | N | N | Y | Y | Y | N | Y | N | Y |
| Circos plot | Y | N | Y | Y | N | Y | Y | N | Y | N | |
| Bubble plot | Y | Y | N | Y | N | N | N | N | N | Y | |
| Sankey plot | Y | N | N | Y | N | N | N | N | N | N | |
| Ridge plot | Y | N | N | N | N | N | N | N | N | N | |
| TF enrichment plot | Y | N | N | N | N | N | N | N | N | N |