preprocess.yaml Reference

This configuration file corresponds to --option=preprocess and controls quality control, filtering, normalization, and dimensionality-reduction preparation.

Parameter	Default	Description
option	preprocess	Fixed identifier for the analysis stage
results_folder	results	Root directory for analysis outputs
data_fold	data	Root directory for raw input data
sample_list	sample.txt	Path to the sample list file
run_type	visium	Spatial transcriptomics platform type
channel	compare_analysis	Single-sample or integrated analysis mode
seg_filter	False	Whether to enable sample-specific filtering thresholds
filter_list	False	Path to a custom threshold file
min_genes	3	Minimum number of genes required per spot or cell
min_cells	3	Minimum number of cells in which a gene must appear
mt_threshold	80.0	Upper limit for mitochondrial proportion filtering
variable	False	Whether to perform highly variable gene selection
NEIGHBORS	10	Number of neighbors used for the neighbor graph
batch_method	harmony	Batch correction method for multi-sample analysis
n_top_genes	3000	Number of highly variable genes
n_comps	50	Number of PCA components
sketch	False	Whether to enable sketch-based analysis for large datasets
sample_rate	0.30	Sampling fraction

Tuning suggestions

1. When sample quality differs substantially across samples, enable seg_filter to apply differential filtering.

2. For multi-sample analyses, using batch_method is usually recommended to reduce batch effects.

3. For datasets containing millions of cells, enable sketch to improve iteration speed.