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bioRxiv · 10.1101/2024.12.16.628633

GenePioneer: A Comprehensive Python Package for Identification of Essential Genes and Modules in Cancer

Taheri, G.·Haerianardakani, A.
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Abstract

SummaryWe propose a network-based unsupervised learning model to identify essential cancer genes and modules for 12 different cancer types, supported by a Python package for practical application. The model constructs a gene network from frequently mutated genes and biological processes, ranks genes using topological features, and detects critical modules. Evaluation across cancer types confirms its effectiveness in prioritizing cancer-related genes and uncovering relevant modules. The Python package allows users to input gene lists, retrieve rankings, and identify associated modules. This work providing a robust method for gene prioritization and module detection, along with a user-friendly package to support research and clinical decision-making in cancer genomics. AvailabilityGenePioneer is released as an open-source software under the MIT license. The source code is available on GitHub at https://github.com/Golnazthr/ModuleDetection Contactgolnazt@kth.se and haerian.amirhossein@gmail.com

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Taheri, G., Haerianardakani, A.. 2024-12-21. GenePioneer: A Comprehensive Python Package for Identification of Essential Genes and Modules in Cancer. https://doi.org/10.1101/2024.12.16.628633

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