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

• Quickstart
• Overview
• Instructions
• Support
• Citation
• URLs

Quickstart

Step 1: Pre-install Required Package

install.packages("BiocManager")
BiocManager::install(version = "3.19")
BiocManager::install("qvalue")

Step 2: Install the ShiNyP Package from GitHub

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

Step 3: Start the ShiNyP Platform

library(ShiNyP)
ShiNyP::run_ShiNyP()

Step 4: Run ShiNyP Analysis

Input your SNP data in VCF format, or feel free to use our Demo Data.

Overview

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

Analysis: Data QC, Population genetics analysis, Core collection…

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

• Statistical and computational exploration
• Customizable visualization options
• Publication-ready figures and tables
• Analyzed R data objects
• Auto-generate customized preliminary results
• AI-driven report - powered by OpenAI

Instructions

For detailed instructions on each feature, please visit the User Guide.

Support

If you encounter any issues or have suggestions for new features, please submit a report through our Feedback Form.

Citation

Huang et al. (upcoming 2024) ShiNyP: An Interactive Shiny-based Platform for Genome-Wide SNP Analysis and Visualization
Under Review…

URLs

• Journal Article: Under Review…
• User Manual: https://github.com/TeddYenn/ShiNyP
• Demo Datasets: https://reurl.cc/QEx5lZ
• Demo Platform: https://teddyhuang.shinyapps.io/ShiNyP/
• Feedback Form: https://forms.gle/GPCggSo5czyNLfoB7
• GitHub Repository: https://github.com/TeddYenn/ShiNyP