Refactoring preprocess_data, calculate_entropy and commitment_score - #83
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…fix var_names and W handling, ensure obs annotations exist, use MODEL consistently
Change score definition so that higher score = higher commitment
Add as its own function to regvelo tools
Remove sig_palette from function call
Added section about RegVelo agentic workflow via Biomni lab.
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Thank you Emma! |
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Refactored preprocess_data with new parameter return_velo_genes to get velocity-informative gene list. Refactored calculate entropy to return maximum entropy for scaling output plot. Refactored commitment score to change implementation to 0 = low commitment, 1= high commitment. Moved visits_diff_per_tf to new function in tools from markov_density_screening