ShiNyP: Unlocking SNP-Based Population Genetics-An AI-Assisted Platform for Rapid and Interactive Visual Exploration.

Abstract

Efficient and accessible analysis of genome-wide single nucleotide polymorphism (SNP) data is vital for advancing molecular biology, evolutionary genetics, and breeding research. However, current analytical pipelines are often fragmented and require command-line expertise, limiting accessibility for many researchers. Here, we present ShiNyP, an interactive R/Shiny platform that integrates all popular SNP analysis modules within a single and intuitive user interface, supporting the entire workflow from data import and quality control to population structure inference, diversity analysis, selective scan, and core collection. ShiNyP accommodates datasets from haploid, diploid, and polyploid species and automates the generation of over 70 publication-ready visualizations and summary tables. A distinctive feature is its automated report module, which employs generative AI to deliver structured, interpretable narratives of complex statistical results. Performance benchmarks demonstrate that ShiNyP efficiently processes large-scale datasets on standard hardware. The ShiNyP platform is freely available at https://github.com/TeddYenn/ShiNyP, providing an efficient, reproducible, and user-friendly solution for population genomics research.