Rscript cell-communication.R <input> <outdir> <project> [options]

scRNA-seq Cell Communication Analysis using CellChat

positional arguments:
  infile         input SeuratObject rds, Idents should be set to celltype
  outdir         output result folder
  project        project name

flags:
  -h, --help     show this help message and exit

optional arguments:
  -x, --opts     RDS file containing argument values
  -m, --method   current support is CellChat [default: CellChat]
  -s, --species  human or mouse [default: human]
  -c, --cores    cores to do parallel [default: 20]

 # SingleR
 Rscript cell-communication.R examples/two-samples.rds ~/tests/communication test

communication
├── test.interaction.cellchat.init.rds
├── test.interaction.cellchat.infer.rds
├── test.interaction.cellchat.inferred_network_ligands.tsv
├── test.interaction.cellchat.inferred_network_pathway.tsv
└── test.interaction.cellchat.output.pdf