Guidance on filtering CellChatDB for targeted panels

[AlbertoFabbri93]

Hi,

I am analyzing data from a targeted gene panel (CosMx/Nanostring) using CellChat. Since many ligands and receptors in CellChatDB are not included in my panel, I am considering filtering the database to retain only interactions where the ligand and all receptor subunits are present in the measured gene set.

The current vignette explains how to subset by annotation (e.g., Secreted Signaling) but does not discuss filtering by measured genes. Could you clarify whether you recommend pre-filtering the database in this scenario, or if CellChat’s built-in expression filtering is sufficient?

Thanks you!

[sqjin]

@AlbertoFabbri93 The CellChat’s built-in expression filtering is sufficient, which will retain only interactions where the ligand and all receptor subunits are present in the measured gene set.