Version Compatibility

Reference examples tested with: MAGeCK 0.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+, statsmodels 0.14+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CRISPR Screen Hit Calling

"Identify essential genes from my CRISPR screen" → Call significant gene hits from sgRNA count data using statistical methods that account for guide-level variability and multiple testing.

• CLI: BAGEL.py bf for Bayes factor essentiality scoring
• Python: drugZ for fold-change based analysis

BAGEL2 Analysis