Cell-cell communication
The cell_communication pipeline scores immune ligand-receptor signaling and cytokine networks. It is the canonical shared engine used by Oncology.
Inputs
| Input | Description |
|---|---|
expression_path or expression_rows | Per-cell expression table |
metadata_path or metadata_rows | Cell metadata with cell type and optional condition |
ligand_receptor_path | Optional ligand-receptor table |
condition_column | Optional condition field for comparison |
Outputs
- ligand-receptor interaction scores
- sender/receiver network summaries
- pathway aggregation
- cytokine-specific network subset
- ligand activity scores using built-in target priors
- comparative deltas between conditions
- interpretation notes
Reference methods
The implementation is inspired by CellPhoneDB-style ligand-receptor scoring, NicheNet-style ligand activity, and CellChat-style pathway aggregation. It is a tabular research workflow, not a causal signaling proof.