Installation and usage
=========================================

The package can be installed from PyPI or directly from GitHub. It requires a Python version of 3.10 or newer. It is based on NetworkX and pandas and requires Cytoscape for visualization. The latter can be downloaded from `here <https://cytoscape.org/download.html>`_.

.. code-block:: bash

   python -m pip install perturbationx # PyPI
   python -m pip install git+https://github.com/mikethenut/perturbationx # GitHub


An example Jupyter notebook `example.ipynb <https://github.com/mikethenut/perturbationx/blob/main/example.ipynb>`_ is available for step-by-step instructions on how to use the package. For advanced usage, refer to the documentation and the `Master's thesis  <https://github.com/mikethenut/perturbationx/blob/main/Integration%20of%20gene%20expression%20data%20with%20causal%20networks.pdf>`_.