jupyter-pathway

Canonical pathway visualization and analysis

Getting Started

Prerequisites

You must already have Jupyter notebook installed. Visit here for more information.

Install pandas, bioservices, and mygene for data processing.

pip install pandas
pip install bioservices
pip install mygene

To use the visualizations module, install networkX, visJS2jupyter and spectra.

pip install networkx
pip install visJS2jupyter
pip install spectra

Installation

You can install jupyterPathway using pip:

pip install jupyterPathway

To import pathwayVisualization, use the following:

from jupyterPathway.jupyterPathwayFunctions import pathwayVisualization

Walkthrough

Sample notebook visualizing MAPK Signaling Pathway: https://bl.ocks.org/lilithhuang/raw/cb18b4175b0034fc04f3aca0a992f479/

Sample notebook visualizing Apoptosis Pathway: https://bl.ocks.org/lilithhuang/raw/849c7e612fd685d2e2fd5e8af4aadfe1/