PyPanda: a Python Package for Gene Regulatory Network Reconstruction

TL;DR

PyPanda is an optimized Python package for gene regulatory network inference using PANDA, offering faster performance and enhanced analysis features compared to the original C++ implementation.

Contribution

This work introduces PyPanda, a Python version of PANDA, improving speed and adding new network analysis capabilities for gene regulatory network reconstruction.

Findings

PyPanda runs faster than the original C++ version.

PyPanda includes additional features for network analysis.

The package is freely available as open source.

Abstract

PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data. PANDA was originally coded in C++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C++ version and includes additional features for network analysis. Availability: The open source PyPanda Python package is freely available at https://github.com/davidvi/pypanda. Contact: d.g.p.van ijzendoorn@lumc.nl