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User Guide for ShiNyP v1.2.0: SNP Analysis and Visualization Platform

Welcome to ShiNyP

ShiNyP-icon

This work, primarily authored by Yen-Hsiang Huang from the Department of Agronomy, National Chung Hsing University, Taiwan, is licensed under the GNU Affero General Public License.

Last Updated: May 2026

Overview

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

📄 Input: Genome-wide biallelic SNP in Variant Call Format (VCF) file.
📊 Analysis: Data QC, population genetics analysis, core collection, and more.
📋 Output: Publication-ready figures, tables, R objects, and free AI-driven report.

Publication

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—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

Aug 2024: alpha version
Oct 2024: v0.1.0
Feb 2025: v0.1.1
Apr 2025: v0.2.0
- Enhanced AI report functionality with new options and models.
- Improved readability of preliminary results.
- Added more methods for constructing core SNP set.
- Added the Docker-based installation.
May 2025: v1.0.0 on GitHub.
- Introduced the new ShiNyP AI chatbot.
- Enhanced AI report features and deprecated older AI models.
- Added publication details.
- Made UI/UX improvements.
- Fixed several bugs.
Jun 2025: v1.1.0 on GitHub.
- Enhanced AI report features.
- Enhanced ShiNyP AI chatbot.
- Made UI/UX improvements.
- Fixed several bugs.
Oct 2025: v1.1.1 on GitHub.
- Made UI/UX improvements.
- Fixed several bugs.
- Added flexible download options.
- Added defensive & error trapping codes.
🆕 May 2026: v1.2.0 on GitHub.
- Global AI Sync.
- Fixed several bugs.

🔽 🐣 ShiNyP AI Chatbot!


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

AI Activation

To use the AI features (AI chatbot and AI reporting), you need to configure your AI model and API key on the Home page.

  1. Go to the Home page.
  2. Find the AI Activation section.
  3. Click Activate Now! to upload your API key and select your preferred model.
  4. Once activated, your settings will sync across the platform.

This is the User Guide site for ShiNyP, live at GitHub Page.