Run CellChat

Run CellChat

Usage

run_cellchat(
  gene_expr,
  annot,
  interactions_db,
  output_dir = ".",
  min_cells = 5,
  n_perm = 1000
)

Arguments

gene_expr

seurat object with gene expression (rds file)

annot

Column in metadata containing the cell type labels

interactions_db

(custom) CellChat database

output_dir

output directory for saving output (default = '.')

min_cells

Minimum number of cells required in each cell group for cell-cell communication (default = 5)

n_perm

Number of permutations for permutation testing (default = 1000)