Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pysam 0.22+, 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
• 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.

Ribosome Periodicity Analysis

"Check if my Ribo-seq data shows triplet periodicity" → Validate Ribo-seq library quality by verifying 3-nucleotide translocation patterns and calculating P-site offsets from metagene profiles.

• Python: plastid for P-site offset calculation and metagene analysis

3-Nucleotide Periodicity

Goal: Verify that Ribo-seq reads exhibit the expected 3-nucleotide translocation pattern characteristic of active translation.