Version Compatibility

Reference examples tested with: BioPython 1.83+, DESeq2 1.42+, 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
• 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.

ORF Detection

"Detect translated ORFs from my Ribo-seq data" → Identify actively translated open reading frames including uORFs and novel ORFs using 3-nucleotide periodicity as evidence of active translation.

• CLI: RiboCode for periodicity-based ORF detection
• R: ORFik for ORF quantification and annotation

RiboCode Workflow