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:

.. code:: shell

   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 

.. image:: https://zenodo.org/badge/753478555.svg
   :target: https://zenodo.org/doi/10.5281/zenodo.10964743

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

.. code-block:: text

    @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}
    }