pykegg¶
pykegg is a Python library for visualization and analysis of KEGG information.
Motivation¶
KEGG information (especially KGML) can be parsed effortlessly by the great package biopython. The package has a built-in module KGML_vis. Also, there are great tutorials for visualizing KEGG information in Python, like this notebook by Dr. Leighton Pritchard, and this tutorial by Dr. Connor Skennerton. There is a nice Python library for visualization of KEGG information with enrichment analysis, keggtools. Extending these packages, I would like to create a package that can address the following problems.
Parse the information from KEGG as a network and conduct network analysis.
Combine with the other omics analysis libraries like
scanpy,PyDESeq2.Visualize the KEGG information by libraries like
OpenCVorplotninein easily customizable ways, using grammer of graphics.
For R environment, please refer to ggkegg.
Analysis¶
Please see notebooks for the visualization example and the example analyses using PyDESeq2, scanpy, and GSEApy.
Note
This project is under active development.
Warning
pykegg uses KEGG API, and is restricted to academic use by academic users belonging to academic institutions.