ShiNyP

ShiNyP integrates common single nucleotide polymorphism analysis modules within an interactive R/Shiny platform to support population genomics research from data import and quality control through population structure inference, diversity analysis, selective scan, and core collection.

Key Features:

• Comprehensive SNP Analysis Workflow: Supports the entire analytical pipeline from data import and quality control to population structure inference, diversity analysis, selective scan, and core collection.
• Ploidy Accommodation: Processes datasets from haploid, diploid, and polyploid species.
• Automated Visualization Generation: Automates the production of over 70 publication-ready visualizations and summary tables.
• Generative AI Report Module: Employs generative AI to deliver structured, interpretable narratives of complex statistical results.
• Performance Benchmarking: Efficiently processes large-scale datasets on standard hardware.

Scientific Applications:

• Population Structure Inference: Enables inference of population genetic structure from genome-wide SNP data.
• Genetic Diversity Analysis: Supports quantification and characterization of genetic diversity within and among populations.
• Selective Scan Analysis: Facilitates detection of genomic regions under selection.
• Core Collection Construction: Assists in identifying representative subsets of germplasm collections for conservation and breeding.
• Molecular Biology and Evolutionary Genetics Research: Advances research in molecular biology, evolutionary genetics, and breeding through accessible population genomics analysis.

Methodology:

ShiNyP is implemented as an interactive R/Shiny platform that integrates common SNP analysis modules; specific algorithmic details of individual analytical methods are not explicitly stated in the sources.