Table 1.
Summary of properties and functionalities for all benchmarked CCI inference methods
| Methods | Properties | Functions | ||||||
|---|---|---|---|---|---|---|---|---|
| CCI scorea | Spatial transcriptomics data | Spatial slices integration | Multi-subunit | Intracellular signaling | In silico receptor blocking | Long-/short-range interactions | Dynamic animation | |
| CellAgentChat | Individual cell | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ |
| CellChat | Cell population | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ |
| CellPhoneDB | Cell population | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ |
| NICHES | Individual cell | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
| COMMOT | Individual cell | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ |
| Scriabin | Individual cell | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ |
| Connectome | Cell population | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ |
| SingleCellSignalR | Cell population | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ |
| NATMI | Cell population | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ |
| scSeqComm | Cell population | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
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Note: Features of CellAgentChat features include integration of multiple spatial slices, single-cell resolution, in silico receptor blocking, identification of short- and long-range interactions, and dynamic animation of CCIs over time.
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aIndividual cell CCI score can be aggregated to obtain cell population CCI scores.
