pFLEX – a Python library for fast functional evaluation of genetic networks at the biological module-level

Abstract

Genetic networks derived from omics data are a powerful tool for systematic gene function prediction. Performance evaluation of such predictions is crucial to judge the data and computational pipeline for network construction, but unbalanced functional standards often cause hidden evaluation biases. To visualize and mitigate such biases, we previously developed the R package FLEX. Here, we present the pFLEX genetic network benchmarking tool as Python library with new and improved functionality. pFLEX improves overall runtime 4.1 to 15.8-fold. It offers additional evaluation metrics that allow for easy comparison of precision recall performance at the complex or pathway resolution between genetic networks. We demonstrate the utility of pFLEX for evaluating tissue-specific co-essentiality networks and data normalization strategies of the Cancer Dependency Map, as well as for cell line-specific Perturb-Seq-derived networks. This illustrates the requirement for biological module-resolved precision recall metrics in pFLEX for sensitive and fast evaluation of genetic networks. Availability and ImplementationpFLEX is available under the MIT license at https://github.com/billmannlab/pFLEX and the pFLEX version used in this manuscript along with benchmarking code for the analyses presented in this manuscript are archived at https://doi.org/10.5281/zenodo.20632868.