Preprocessing Overview

The preprocessing module handles data loading, quality control, normalization, alignment, batch correction, and merging.

Pipeline Position

Stages

Stage	Purpose	Input	Output
Data Loading	Load and validate data	Raw matrices	Verified metadata
Cell QC	Remove low-quality cells	Cell matrices	Filtered matrices
Normalization	Within-sample normalization	Filtered data	Normalized data
Alignment	Cross-sample alignment	Normalized data	Aligned data
Batch Correction	Remove batch effects	Aligned data	Corrected data
Data Merging	Merge into AnnData	All stages	merged.h5ad

CLI Usage

celltype-refinery preprocess \
  --input data/ \
  --config preprocess.yaml \
  --out output/preprocessed

Python API

from celltype_refinery.core.preprocessing import PreprocessingPipeline

pipeline = PreprocessingPipeline(config_path="preprocess.yaml")
adata = pipeline.run(input_dir="data/", output_dir="output/")