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. 2023 Feb 3;39(2):btad064.
doi: 10.1093/bioinformatics/btad064.

PyGenePlexus: a Python package for gene discovery using network-based machine learning

Christopher A Mancuso  1   2 , Renming Liu  1 , Arjun Krishnan  1   3
Affiliations

PyGenePlexus: a Python package for gene discovery using network-based machine learning

Christopher A Mancuso et al. Bioinformatics. .

Abstract

Summary: PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest through a molecular interaction network informed supervised machine learning model. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes.

Availability and implementation: https://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Running PyGenePlexus on the command line. (A) The GenePlexus model can be run with one simple command that (B) allows the user to select a number of different parameters and (C) obtain the results that are conveniently saved to the specified directory
See this image and copyright information in PMC

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