scRNA-Seq batch effect checker

This is my mini_toolkit to check for batch effect for scRNA-Seq dataset

Step 1: evaluate_batch_effects.py Step 2: apply_harmony_correction.py

# Provide recommendation
Overall batch effect score : 0-1 scale, higher means stronger batch effect
if batch_effect_score < 0.3:
    print("RECOMMENDATION: Batch correction likely NOT needed")
    print("- Your data shows minimal batch effects")
    print("- Proceed without Harmony or other batch correction methods")
elif batch_effect_score < 0.6:
    print("RECOMMENDATION: Moderate batch effects detected")
    print("- Try analysis both with and without batch correction")
    print("- Consider using Harmony with default parameters")
else:
    print("RECOMMENDATION: Strong batch effects detected")
    print("- Batch correction is highly recommended")
    print("- Use Harmony or another batch correction method")
    print("- Consider higher theta parameter in Harmony (e.g., 2.0) for stronger correction")

print("\nSee generated plots for visual assessment of batch effects")