ccc
Analyze cell-cell communication using methods like cellphonedb, cellchat, or connectome. Group cells by annotations, filter results by expression, and identify ligand-receptor interactions.
Instructions
Cell-cell communication analysis with one method (cellphonedb, cellchat,connectome, natmi, etc.)
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| base | No | Exponent base used to reverse the log-transformation of the matrix. Relevant only for the `logfc` method. | |
| de_method | No | Differential expression method used to rank genes according to 1vsRest. | t-test |
| expr_prop | No | Minimum expression proportion for the ligands and receptors in the corresponding cell identities. Set to 0 to return unfiltered results. | |
| groupby | Yes | Key to be used for grouping cells (e.g., cell type annotations). | |
| inplace | No | Whether to store results in place, or return them. | |
| key_added | No | Key under which the results will be stored in adata.uns. | liana_res |
| layer | No | Layer in AnnData.layers to use. If None, use AnnData.X. | |
| method | No | cell-cell communication method | cellphonedb |
| min_cells | No | Minimum cells per cell identity to be considered for downstream analysis. | |
| n_jobs | No | Number of jobs to run in parallel. | |
| n_perms | No | Number of permutations for the permutation test. Relevant for CellPhoneDB method. | |
| resource_name | No | Name of the resource to be used for ligand-receptor inference. See `li.rs.show_resources()` for available resources. | consensus |
| return_all_lrs | No | Whether to return all ligand-receptor pairs, or only those that surpass the expr_prop threshold. | |
| seed | No | Random seed for reproducibility. | |
| supp_columns | No | Additional columns to be added from methods in liana, or columns from scanpy.tl.rank_genes_groups. | |
| use_raw | No | Use raw attribute of adata if present. | |
| verbose | No | Whether to print verbose output. |