Version Compatibility

Reference examples tested with: ggplot2 3.5+

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

• 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.

Differential m6A Analysis

"Find differential m6A sites between my conditions" → Identify RNA methylation changes between experimental groups by comparing MeRIP-seq IP/input ratios across conditions with statistical testing.

• R: exomePeak2::exomePeak2() with contrast design for differential peaks

exomePeak2 Differential Analysis

Goal: Identify m6A sites that differ in methylation level between experimental conditions from MeRIP-seq data.