PerturbationX is a package for analyzing causal networks in combination with gene expression data. It is based on the TopoNPA algorithm. It was developed as part of a Master's thesis at the University of Ljubljana, Faculty of Computer and Information Science and in collaboration with the National Institute of Biology.
The package can be installed from PyPI or directly from GitHub. It requires a Python version of 3.10 or newer. It is based on NetworkX and pandas and requires Cytoscape for visualization. The latter can be downloaded from here.
python -m pip install perturbationx # PyPI
python -m pip install git+https://github.com/mikethenut/perturbationx # GitHubAn example Jupyter notebook example.ipynb is available for step-by-step instructions on how to use the package. For advanced usage, refer to the documentation and Master's thesis.
No paper describing the package has been published yet. If you use this package in your research, please cite the following Zenodo DOI:
@software{rajh2023perturbationx,
author = {Rajh, Mihael and Bleker, Carissa Robyn and Curk, Tomaž},
title = {PerturbationX},
year = 2023,
publisher = {Zenodo},
version = {v1.0.1},
doi = {10.5281/zenodo.10073529},
url = {https://doi.org/10.5281/zenodo.10073529}
}