bio-single-cell-cell-communication

CellChat (R)

Goal: Infer and quantify intercellular communication networks from scRNA-seq data using curated ligand-receptor databases.

Approach: Create a CellChat object from a Seurat object with cell type labels, select a signaling database subset, identify overexpressed ligands/receptors, compute communication probabilities using the trimean method, then aggregate into pathway-level networks.

library(CellChat)
library(Seurat)

## Set ligand-receptor database

CellChatDB <- CellChatDB.human  # or CellChatDB.mouse
cellchat@DB <- CellChatDB

## Subset to secreted signaling (optional)

CellChatDB.use <- subsetDB(CellChatDB, search = 'Secreted Signaling')
cellchat@DB <- CellChatDB.use