Run CellChat — run_liana • scrnaseq.cellcomm

Run CellChat

Usage

run_liana(
  gene_expr,
  interactions_db,
  annot,
  output_dir = ".",
  min_cells = 5,
  min_pct = 0.1,
  n_perm = 1000
)

gene_expr: seurat object with gene expression (rds file)
interactions_db: (custom) CellChat database (rds file)
annot: Column in metadata containing the cell type labels
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)
min_pct: Minimum fraction of cells expressing a gene (default = 0.1 = 10%), max = 1
n_perm: Number of permutations for permutation testing (default = 1000)