CaGraph

Graph theory analysis and visualization package for calcium imaging timeseries data. The package makes it simple for experimental researchers to generate graphs of functional networks and inspect their topology, using NetworkX to compute useful graph theory metrics. Bokeh is used to assist with interactive plotting of graph networks.
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Table of Contents

1. About The Project
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. License
5. Contact
6. Acknowledgements

About The Project

Getting Started

To get a local copy up and running follow these simple steps.

Prerequisites

A list of software required for the CaGraph project and how to install the packages.

• networkx

  pip install networkx

• bokeh

  pip install bokeh

• numpy

  pip install numpy

• matplotlib

  pip install matplotlib

• pynwb

  pip install pynwb

• scipy

  pip install scipy

• seaborn

  pip install seaborn

• statsmodels

  pip install statsmodels

Installation

1. Clone the repo

   git clone https://github.com/vporubsky/CaGraph.git

2. Install via PyPI

   pip install cagraph

Usage

Examples of using the package will be added here. Additional screenshots, code examples and demos will be included formally in documentation.

Documentation to be added.

License

Distributed under the MIT License. See LICENSE for more information.

Contact

Veronica Porubksy - verosky@uw.edu

Project Link: https://github.com/vporubsky/CaGraph

Acknowledgements

• Sauro Lab at the University of Washington
• Bruchas Lab at the University of Washington