BioMark: A Web-Based Biomarker Analysis Tool

BioMark is a user-friendly, web-based platform designed to streamline biomarker discovery and analysis from high-dimensional omics data. It aims to empower researchers, especially those without extensive computational expertise, to perform complex analyses such as differential analysis, clustering, and classification with just a few clicks.

🚀 Quick Links

🖥️ Live Tool: https://bioinf.itu.edu.tr/biomark
🎥 Video Tutorial: Watch the full tutorial on YouTube
📄 Sample Analysis Report: View the Sample Analysis Report (Biomarker_Sample_Analysis_Report.pdf)

✨ Key Features

No-Code Interface: Perform advanced analyses entirely through an intuitive web interface.
Multiple Analysis Methods: Supports statistical tests (ANOVA, t-test) and machine learning explainability methods (SHAP, LIME).
Consolidated Ranking: A unique feature to combine and rank biomarker lists from multiple methods for more robust findings.
Interactive Visualizations: Instantly generate PCA, t-SNE, UMAP plots, heatmaps, and various SHAP plots.
Automated Reporting: Download a comprehensive PDF report of your entire analysis workflow.

🚀 Getting Started

This repository contains the source code for the frontend and backend components of BioMark.

Clone the repository:

git clone [https://github.com/itu-bioinformatics-database-lab/biomark.git](https://github.com/itu-bioinformatics-database-lab/biomark.git)

Follow the setup instructions within the backend/ and frontend/ directories to run the application locally.

✍️ Citation

If you use BioMark in your research, please cite our work.

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📝 License

This project is licensed under the MIT License. See the LICENSE file for details.