Bioinformatics Analyses - Genotype/Allele and Pathways

Genotype-allele contingency testing with PLINK-R integration and pathway/PPI analysis.

Why I Built This

I kept running into the same gap in genomics work: statistical SNP outputs were easy to generate, but biological interpretation was slow and inconsistent across tools. I built this to connect the full path from genotype and allele testing to pathway and network-level insight in one reproducible workflow. The goal was to make results easier to validate, explain, and reuse across studies.

What I Implemented

  • End-to-end genotype and allele contingency testing with 2x3 and 2x2 chi-square analysis.
  • PLINK + R pipeline for quality checks and automated QQ/Manhattan plotting.
  • Pathway and network interpretation with Enrichr, STRING, and DAVID.

Why It Matters

This project helped me connect raw association signals to biologically meaningful interpretations, which is the part that usually takes the most manual effort.

Outcome

A repeatable analysis flow that can be reused for SNP-focused studies where both statistical rigor and biological context matter.