If the experiments include anti-ligand treatment, is it still possible to apply cell-cell analysis to single-cell data? For example, if a ligand is blocked, it won't be able to bind to its receptor. However, as far as I understand, cell-cell interaction analysis tools calculate interactions based solely on the expression levels of ligands and receptors. For instance, if cell A expresses TGFB1 (the ligand) and cell B expresses TGFBR1 (the receptor), then, based on their high expression levels, they would likely be considered to have a high probability of communication.
But if a receptor has been blocked in the experiment, will cell-cell interaction analysis provide realistic results? After all, the cell may still be overexpressing the receptor, but the interaction may not be occurring due to the treatment. Which tools take this situation into account that you can recommend?
