Non-Coding RNA Analysis Pipeline for identifying, annotating, and interpreting non-coding RNAs and their biological roles. Covers microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and other ncRNA classes. Key principles : 1. Class determines function — miRNAs repress mRNA translation; lncRNAs have diverse mechanisms (scaffolds, guides, decoys, enhancers); rRNAs/tRNAs are structural 2. Targets matter more than the ncRNA itself — for miRNAs, the regulated mRNA targets determine the phenotype 3. Expression context is critical — ncRNAs are highly tissue/cell-type specific 4. Conservation indica…