proteINET Documentation
=======================

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

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   getting_started
   api/index


Quick Start
-----------

.. code-block:: python

    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
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`