Getting started

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” 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/, together with tutorials.