Overview of py4cytoscapeΒΆ


py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over 250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

py4cytoscape provides:

  • functions that can be leveraged from Python code to implement network biology-oriented workflows;

  • access to user-written Cytoscape Apps that implement Cytoscape Automation protocols;

  • logging and debugging facilities that enable rapid development, maintenance, and auditing of Python-based workflow;

  • two-way conversion between the igraph and NetworkX graph packages, which enables interoperability with popular packages available in public repositories (e.g., PyPI); and

  • the ability to painlessly work with large data sets generated within Python or available on public repositories (e.g., STRING and NDEx);

  • execute Python code on the Cytoscape workstation or in Jupyter Notebooks on local or remote servers.

With py4cytoscape, you can leverage Cytoscape to:

  • load and store networks in standard and nonstandard data formats;

  • visualize molecular interaction networks and biological pathways;

  • integrate these networks with annotations, gene expression profiles and other state data;

  • analyze, profile, and cluster these networks based on integrated data, using new and existing algorithms.