limmaGenie-react-python-app
🚀 Try at limmaGenie
🧞♀️ live demo
Your AI-powered assistant for differential expression analysis using the limma package.
Try it here here:
📌 About Us
limmaGenie is a web-based assistant built to help researchers perform differential expression analysis using limma. Whether you’re new to bioinformatics or an experienced researcher, limmaGenie provides step-by-step guidance to:
- Design your experiment
- Generate R code using
limma - Understand and interpret outputs across RNA-seq, microarrays, and other omics data
Built with LLM-powered intelligence and deployed as a lightweight app, it’s designed to democratize omics analysis.
⚙️ How it works
🛠️ How to Install
-
Clone the Repository:
> git clone https://github.com/Somu796/limmaGenie-react-python-app.git > cd limmaGenie-react-python-app -
Write a .env file:
LIMMAGENIE_OPENAI_API_KEY=Your_OPENAI_API_KEY MONGODB_CONNECTION_STRING=Your_Database_Connection_String OPENAI_MODEL_NAME=gpt-4o-mini EMBEDDING_MODEL_NAME=text-embedding-ada-002 -
Run the App:
> docker compose up
🧠 What Tech Stack?
- Frontend & UI: React.js
- Backend Logic: Python + FastAPI + LangChain
- LLM Integration: OpenAI + LangChain + Prompt Engineering
- Knowledge Curation: Unstructured + BeautifulSoup
- Search Integration: DuckDuckGo + BeautifulSoup
- Database: MongoDB (secure access required)
- Contenarisation: Docker Compose
🔐 To Get DB Access
To get access to the database for full functionality, please email:
📧 bkushagra100@gmail.com 📧 sudiptakh037@gmail.com
📘 Citations & Learning Resources
Learn more about limma and associated tools here:
- limma User’s Guide (Bioconductor)
- Design Matrix Guide for Gene Expression
- RNA-seq Analysis with limma, Glimma, and edgeR
👨🔬 Built By
- Sudipta Kumar Hazra – MSc (Research) Student, UCC and Teagasc, Ireland
- Kushagra Bhatnagar – Machine Learning Scientist
We’re committed to building smarter and simpler tools for the omics research community.
💬 Thanks for Visiting
If you find this useful, ⭐ star the repo and feel free to contribute!
Sample Questions
- I have 3 treatments, stress or not stress, grass fed or hay, bull or cow, help me to build a limma model for the analysis of my proteomics data