Version Compatibility

Reference examples tested with: DESeq2 1.42+, numpy 1.26+, pandas 2.2+

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

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

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

Translation Efficiency

"Calculate translation efficiency from my Ribo-seq and RNA-seq" → Compute the ratio of ribosome occupancy to mRNA abundance per gene to identify translational regulation independent of transcription changes.

• R: riborex for differential TE with DESeq2 backend
• Python: Ribo-seq/RNA-seq count ratio with statistical testing

Concept