Overview of py4cytoscapeΒΆ
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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.