NetGrep

Collection of functions for large-scale downstream gene regulatory network analysis. Functions are currently adapted for use with pySCENIC.

App Changelog

03.19.2026: Standalone NetGrep app is now available for testing! Features include:

• Weight-based edge filtering
• Custom layouts for GRNs (Spiral and GRN-Clusters)
• Aesthetic customization of network graphs
• Regulon query and subnetwork generation. - Regulon component export as .csv
• Gene of interest query - Subnetwork of adjacencies, direct/indirect TF regulators.

Usage

• For using pre-existing functions in python to generate .gexf files to visualize in Gephi. See Functions
• For using the standalone app with built in network visualizer.

  • Clone the github repository

  • Use the netgrep .yml to to create a conda environment/equivalent with the required packages. Activate environment.

  • launch the standalone_app.py via the following terminal command:

    python standalone_app.py
    

  • Load testing .csv and/or regulon_object.pkl. Or supply your own. (More documentation to come)

Previews

Note: App is in early development and subject to change

Explore and adjust whole network diagrams.

Visualize subnetworks of regulons of interest.

Query genes of interest and visualize meaningful regulatory connections.