Reference

Detailed parameter tables, function signatures, and module-level documentation.

Page	What you’ll find
Configuration	All parameters in genecircuitry/config.py — defaults, descriptions, runtime update pattern
API Reference	Public function signatures for all modules
ATAC Peaks Processing	process_atac_peaks() — BED file → TF motif matrix for CellOracle

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Table of contents

• Configuration
• API Reference
• ATAC Peaks Processing