proteINET Documentation

A toolkit to fetch, analyze and visualize protein-protein interaction (PPI) networks using the STRING database.

Contents:

Quick Start

from graph.StringLoader import StringLoader
from graph.PPINetwork import PPINetwork
from visual.ReportGenerator import ReportGenerator

# Fetch network from STRING
loader = StringLoader(protein_query=["TP53", "BRCA1"], species=9606, add_nodes=20)
data = loader.retrieve_data().standardize_data_format().get_data()

# Build network and compute metrics
ppin = PPINetwork(data=data)
ppin.compute_all_node_metrics(weighted=False)
ppin.compute_all_edge_metrics(weighted=False)

# Generate interactive HTML report
ReportGenerator().add_cytoscape_html_report(
    ppin, title="STRING Protein Network"
).generate_report_file("report.html")

Features

  • Query STRING-DB (functional or physical networks)

  • Compute global, node and edge network metrics

  • Export nodes/edges/graph (CSV, GraphML) for Cytoscape

  • Run GSEA (via gseapy) on ranked gene lists

  • Generate interactive HTML reports with Cytoscape.js visualizations

Indices and tables