Ligand-to-target hypotheses

Use this workflow when communication results need a mechanistic explanation. It ranks candidate sender ligands against receiver target-gene programs and returns ligand-target and ligand-receptor-target evidence that can be reviewed alongside cell-cell communication outputs.

Research question

Which ligands from candidate sender populations best explain receiver target genes, and which ligand-receptor-target chains should be prioritized for follow-up?

Use case

Use this after annotation and communication when a pathway-level signal needs candidate ligand mechanisms. Examples include myeloid ligands that may drive exhausted T cell targets, stromal ligands linked to inflammatory programs, or B cell signals associated with tissue organization.

Suggested path

1. Register expression and metadata datasets with cell-type labels.
2. Define sender cell types, a receiver cell type, and target genes or a target-gene file.
3. Run Ligand Activity Inference.
4. Review ligand rankings, ligand-target matrix rows, ligand-receptor-target paths, and interpretation notes.
5. Pair the result with cell_communication when you want expression-supported sender/receiver context.

Outputs to cite

• ligand activity score
• sender expression score
• receiver receptor score
• receiver target score
• target coverage
• ligand-target prior weight
• ligand-receptor-target path score