Installation

Requirements

HELP depends on the following packages:

  • numpy

  • pandas

  • typing

  • matplotlib

  • skimage

  • sklearn

  • tqdm

  • lightgbm

  • tabulate

  • networkx

  • karateclub

  • ipywidgets

  • supervenn

Pip

HELP allows pip-based installation, please use the following command:

pip install git+https://github.com/giordamaug/HELP.git

Cite

If you use want to reference the HELP software, please cite the DOI: doi/10.5281/zenodo.10964743

https://zenodo.org/badge/753478555.svg

If you want to cite the work in which the HELP software was first proposed and described, please cite the following article:

@article {Granata2024.04.16.589691,
    author = {Ilaria Granata and Lucia Maddalena and Mario Manzo and Mario  Rosario Guarracino and Maurizio Giordano},
    title = {HELP: A computational framework for labelling and predicting human context-specific essential genes},
    elocation-id = {2024.04.16.589691},
    year = {2024},
    doi = {10.1101/2024.04.16.589691},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2024/04/20/2024.04.16.589691},
    eprint = {https://www.biorxiv.org/content/early/2024/04/20/2024.04.16.589691.full.pdf},
    journal = {bioRxiv}
}