Version Compatibility

Reference examples tested with: BioPython 1.83+, numpy 1.26+, scipy 1.12+

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

• Python: pip show <package> then help(module.function) to check signatures

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

Ribosome Stalling Detection

"Find ribosome pause sites in my data" → Detect codon-level ribosome stalling and pausing events from Ribo-seq footprint density, identifying positions with abnormally high ribosome occupancy.

• Python: plastid for codon-resolution density calculation, scipy for statistical scoring

Concept