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User Guide for ShiNyP: 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 General Public License.

Last Updated: April 2025

This is the user guide site for ShiNyP, live at https://teddyenn.github.io/ShiNyP-guide/.

ShiNyP

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, data objects, and AI-driven report.

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

Updates

  • Aug 2024: Initial release alpha version on GitHub.

  • Oct 2024: Release v0.1.0 on GitHub.

  • Feb 2025: Release v0.1.1 on GitHub.

    - Simplified workflow for Data Input & Transform.

    - Refined visual elements.

    - Optimized memory usage.

  • Apr 2025: 🆕 Release v0.1.2 on GitHub.

    - Enhanced AI report functionality with new configuration options.

    - Improved the layout of preliminary results for better readability.

    - Added more methods for constructing core SNP set.