GPU-accelerated estimation of gene regulatory networks

Code base for gpuZoo: cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. doi.org/10.1093/nargab/lqac002

Introduction

gpuZoo is a GPU-accelerated implementation of PANDA, PUMA, SPIDER, and LIONESS to generate aggregate and single-sample gene regulatory networks.

This repository contains the code to generate the figures in the paper and the code for benchmarking gpuZoo in MATLAB and Python.

gpuZoo is available through netZooM (> 0.5.2) with a step-by-step tutorial and netZooPy > 0.6.2) with a step-by-step tutorial.

To download the data used for the benchmark, visit the netZoo website.

Issues

Feel free to open an issue here if you have any comment about the benchmarks and here if you have a comment about gpuZoo.