visJS2jupyter

visJS2jupyter provides visualization of biological networks using the vis.js JavaScript library within Jupyter notebooks to support network biology analyses including network overlap analysis, network propagation around focal sets of genes, and co-localization of seed gene sets.

Key Features:

• Visualization with vis.js: Renders biological networks using the vis.js JavaScript library within Jupyter notebook cells for exploratory analysis.
• Network Overlap Analysis: Computes and displays overlaps between networks or gene sets.
• Network Propagation: Performs propagation of information around a focal set of genes to prioritize related genes.
• Seed Gene Co-localization: Identifies and visualizes co-localization of two sets of seed genes within a network.

Scientific Applications:

• Network Biology: Exploration and interpretation of complex biological interactions and mechanisms through network visualization and analysis.
• Gene Prioritization: Prioritization of risk-related genes using network propagation, as demonstrated in an autism case study.
• Hypothesis Generation: Interactive inspection of network structure to support hypothesis generation from molecular and genetic data.

Methodology:

Embeds vis.js-rendered networks into Jupyter notebook cells and implements network overlap analysis, network propagation around focal gene sets, and co-localization analysis of two seed gene sets.