community-explorer 0.1.0

A bioinformatics tool for network analysis and visualization of gene sets.

Community Explorer (cx)

cx is a bioinformatics tool for network analysis and visualization of gene sets. It takes a list of genes, builds a protein-protein interaction network, identifies communities (functional modules) within the network, and performs functional enrichment analysis to uncover the biological significance of these communities.

Features

• Network Analysis: Constructs interaction networks from gene lists using the STRING database.
• Community Detection: Uses the Leiden algorithm to identify densely connected communities of genes.
• Enrichment Analysis: Performs functional enrichment analysis on gene communities using g:Profiler.
• Interactive Visualization: A web-based interface built with Streamlit allows for easy input and visualization of results.

Installation

To install the required dependencies, use pip with the pyproject.toml file:

pip install .

Usage

To run the web application, use the following command:

streamlit run app.py

This will start a local web server and open the application in your browser.