advance_analysis.yaml Reference

This configuration file corresponds to --option=advance_analysis and covers six downstream modules: cellPhoneDB, pysenic, liana, cellchat, cellcharter, and banksy.

Global fields

Parameter	Default	Description
`option`	`advance_analysis`	Fixed stage identifier
`results_folder` / `data_fold` / `sample_list`	`results` / `data` / `sample.txt`	Output directory, data directory, and sample list
`run_type` / `channel` / `runpipe`	`visium_HD` / `single_analysis` / `cellPhoneDB`	Platform type, analysis channel, and downstream module entry point

Module-specific parameters

Parameter	Default	Description
`senic_input` / `tfs_input` / `feather_input` / `motifs_input`	See the generated template	PySCENIC input object and database resource paths
`senic_workers`	`128`	Number of parallel workers for PySCENIC
`cellPhoneDB_input`	`results/.../Colon_Cancer_P2_cellcharter.zarr`	Default input object for CellPhoneDB or LIANA
`counts_data` / `threshold` / `pvalue` / `iterations`	`hgnc_symbol` / `0.1` / `0.05` / `500`	Statistical thresholds and permutation settings for CellPhoneDB
`cpdb_method` / `cpdb_de_method`	`statistical` / `wilcoxon`	CellPhoneDB mode and differential method label
`cell_type1` / `cell_type2` / `gene_family`	`Endothelial` / `Tumor` / `""`	Cell pairs and gene families emphasized in visualization
`liana_method` / `liana_resource_name`	`cellphonedb` / `consensus`	LIANA method and resource database
`liana_expr_prop` / `liana_min_cells` / `liana_use_raw`	`0.1` / `5` / `true`	LIANA filtering thresholds and expression matrix source
`assay` / `species` / `min_cells` / `workers` / `trim` / `interaction_length`	`Spatial` / `human` / `10` / `32` / `0.1` / `150`	CellChat species, statistical, and spatial distance parameters
`max_cluster` / `condition_col` / `sample_col` / `cellcharter_col`	`10` / `condition` / `region` / `spatial_cluster`	CellCharter clustering search and comparison fields
`k_geom` / `max_m` / `nbr_weight_decay` / `lambda_list`	`15` / `1` / `scaled_gaussian` / `[0.8]`	BANKSY neighborhood geometry and spatial weighting parameters

Tuning suggestions

First set runpipe, then focus only on the parameters used by the selected downstream module.
For communication-focused modules, first confirm that celltype_col matches the annotation column in the input object.
For more complex analyses, use absolute paths for database resources to reduce environment-dependent errors.