.. _about:

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Getting started
================

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What is Phasik?
-----------------

The Phasik package was created to infer temporal phases in temporal networks.  It contains various utility classes and functions that can be divided into two main parts:

1. Build, analyse, and visualise temporal networks from time series data.
2. Infer temporal phases by clustering the snapshots of the temporal network.

Phasik was initially created for the analysis presented in the paper "`Inferring cell cycle phases from a partially temporal network of protein interactions <https://doi.org/10.1101/2021.03.26.437187>`_" by Lucas, M., Morris, A., Townsend-Teague, A., Tichit, L., Habermann, B. H., & Barrat, A. (2021), bioRxiv.

Installation 
-------------

Install the latest version of `phasik` with `pip`::

    $ pip install phasik

Alternatively, you can clone the repository manually or with `git`, and then install with `pip`::
    
    $ git clone https://gitlab.com/habermann_lab/phasik.git  
    $ pip install ./phasik
    
You can also simply try `phasik` by cloning the repository without installing the package.

Documentation
--------------

The full documentation of the package is available at `phasik.readthedocs.io/en/latest/ <https://phasik.readthedocs.io/en/latest/>`_, together with tutorials.



