ShiNyP: SNP Analysis and Visualization Platform

Note

🆕 ShiNyP v1.1.1 is now available!

🧬 Quickstart

🚀 Run ShiNyP via R

🚀 Run ShiNyP via Docker

📢 ShiNyP Online Version – Trial Platform

🔸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 ⬅️

🔸Run ShiNyP via R

✅ Prerequisites

• R: Version ≥ 4.4

  ℹ️ Check your current version in R:

  getRversion()

• Bioconductor: Version ≥ 3.20

  ⚠️ Match your Bioconductor version with your R version (e.g., use Bioconductor 3.21 if R = 4.5).

1️⃣ Install Required Packages

install.packages("BiocManager")
BiocManager::install(version = "3.21") # Use the version that matches your R
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 dataset in VCF, or try the built-in demo data.

🔸Run ShiNyP via Docker

If you have 🐳 Docker installed, you can launch ShiNyP without installing R or any packages.

✅ Prerequisite

• Docker

  ℹ️ Verify your Docker installation:

  docker --version

1️⃣ Pull the Docker Image

docker run -d -p 3838:3838 teddyenn/shinyp-platform

2️⃣ Start the ShiNyP Platform

Open your browser and visit 👉 http://localhost:3838.

🔸URLs

🔗 Journal Article: https://doi.org/10.1093/molbev/msaf117

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

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

🔗 ShiNyP Outputs (Demo): https://zenodo.org/records/14813628

🔗 Online Platform (Trial): https://teddyhuang.shinyapps.io/ShiNyP_Demo/

🔗 Docker Image: https://hub.docker.com/r/teddyenn/shinyp-platform/tags

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

🔸Citation

If you use ShiNyP in your research, please cite:

Huang, Y.-H., Chen, L.-Y., Septiningsih E. M., Kao, P.-H., Kao, C.-F. (2025) ShiNyP: Unlocking SNP-Based Population Genetics—An AI-Assisted Platform for Rapid and Interactive Visual Exploration. Molecular Biology and Evolution, 42(6), msaf117. https://doi.org/10.1093/molbev/msaf117

In addition, please acknowledge the R packages utilized in your analysis. The relevant citations and descriptions for each module are detailed in the ShiNyP User Guide.

🔸Updates and Support

If you encounter any issues or have suggestions for new features, please submit a request on the GitHub Issues page or email us at: teddyhuangyh@gmail.com

• Aug 2024: Initial release alpha version.
• Oct 2024: Release v0.1.0.
• Feb 2025: Release v0.1.1.
• Apr 2025: Release v0.2.0.
• May 2025: Release v1.0.0.
• Jun 2025: Release v1.1.0.