ShiNyP: An Interactive Shiny-based Platform for Genome-Wide SNP Analysis and Visualization

Note

🆕 Now available: ShiNyP v0.1.2

• Enhanced AI report functionality with new configuration options and new AI models (Free: Gemini 2.0; GPT-4.1).
• Improved the layout of preliminary results for better readability.
• Added more methods for constructing core SNP set.

🔸Overview

ShiNyP is a platform designed for real-time processing, analysis, and visualization of SNP datasets.

📄Input data: Genome-wide biallelic SNP in Variant Call Format (VCF).

📊Analysis: Data QC, population genetics analysis, core collection, and more.

📋Output: Publication-ready figures, tables, analyzed data objects, and free AI-driven reports.

For detailed instructions on each feature, please visit ➡️ User Guide ⬅️

🔸Quickstart

✅ Prerequisites

• R Version: R ≥ 4.4 (Compatible with Bioconductor version 3.20)
• R Tools (Recommended, but not required).

1️⃣ Install Required Packages

install.packages("BiocManager")
BiocManager::install(version = "3.20")
BiocManager::install(c("qvalue", "SNPRelate", "ggtree", "snpStats"), force = TRUE)

2️⃣ Install the ShiNyP Package

install.packages("remotes")
remotes::install_github("TeddYenn/ShiNyP", force = TRUE)

3️⃣ Start the ShiNyP Platform

library(ShiNyP)
ShiNyP::run_ShiNyP()

4️⃣ Run Analysis on ShiNyP

Input your SNP data in VCF, or feel free to use the built-in demo data.

🔸URLs

▪️ Journal Article

▪️ User Manual: https://teddyenn.github.io/ShiNyP-guide

▪️ Demo Datasets: https://github.com/TeddYenn/ShiNyP_Test/tree/main/inst/demo_data

▪️ ShiNyP Outputs (Samples): https://zenodo.org/records/14813628

▪️ Online Platform (Demo): https://teddyhuang.shinyapps.io/ShiNyP_Demo/

▪️ GitHub Repository: https://github.com/TeddYenn/ShiNyP

🔸Updates

• Aug 2024: Initial release alpha version.
• Oct 2024: Release v0.1.0.
• Feb 2025: Release v0.1.1.
• Apr 2025: Release v0.1.2.

🔸Support

If you encounter any issues or have suggestions for new features, please submit a report through our Feedback Form or email us at: teddyhuangyh@gmail.com

🔸Citation

Huang et al. (upcoming 2025) ShiNyP: An Interactive Shiny-based Platform for Genome-Wide SNP Analysis and Visualization.