GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer.

Haerianardakani A, Taheri G

Bioinform Adv 5 (1) vbaf094 [2025-04-29; online 2025-04-29]

We 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 provides 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. GenePioneer is released as an open-source software under the MIT license. The source code is available on GitHub at https://github.com/Golnazthr/ModuleDetection.

PubMed 40417653

DOI 10.1093/bioadv/vbaf094

Crossref 10.1093/bioadv/vbaf094

pmc: PMC12098931
pii: vbaf094