Metadata-Version: 2.1
Name: xomx
Version: 0.1.2
Summary: xomx: a python library for computational omics
Home-page: https://github.com/perrin-isir/xomx
Author: Nicolas Perrin-Gilbert
License: LICENSE
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas (>=1.3.0)
Requires-Dist: numpy (>=1.21.1)
Requires-Dist: anndata (>=0.7.6)
Requires-Dist: scipy (>=1.4.1)
Requires-Dist: matplotlib (>=3.1.3)
Requires-Dist: scikit-learn (>=0.24.2)
Requires-Dist: joblib (>=1.0.1)
Requires-Dist: requests (>=2.23.0)
Requires-Dist: holoviews (>=1.15.0)
Requires-Dist: bokeh (>=2.4.3)
Requires-Dist: leidenalg (>=0.8.8)

# ![alt text](https://github.com/perrin-isir/xomx/blob/master/logo.png "logo")

![version](https://img.shields.io/badge/version-0.1.2-blue)
[![codestyle](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Documentation](https://img.shields.io/github/actions/workflow/status/perrin-isir/xomx/docs.yml?branch=master&label=docs)](https://perrin-isir.github.io/xomx/)

*xomx* is an open-source python library providing data processing and 
machine learning tools for computational omics, with a 
particular emphasis on explainability.

It relies on [AnnData](https://anndata.readthedocs.io) objects, which makes it
fully compatible with [Scanpy](https://scanpy.readthedocs.io).

*xomx is currently in beta version.*

-----



## Install

<details><summary>Option 1: conda (preferred option)</summary>
<p>

This option is preferred because it relies mainly on conda-forge packages.


    git clone https://github.com/perrin-isir/xomx.git
    cd xomx
    conda update conda
    
Install micromamba if you don't already have it (you can also simply use conda, by replacing below `micromamba create`, `micromamba update` and `micromamba activate` respectively by `conda env create`, `conda env update` and `conda activate`, but this will lead to a significantly slower installation):

    conda install -c conda-forge micromamba

Choose a conda environment name, for instance `xomxenv`.  
The following command creates the `xomxenv` environment with the requirements listed in [environment.yaml](environment.yaml):

    micromamba create --name xomxenv --file environment.yaml

If you prefer to update an existing environment (`existing_env`):

    micromamba update --name existing_env --file environment.yml

Then, activate the `xomxenv` environment:

    micromamba activate xomxenv

Finally, to install the *xomx* library in the activated environment:

    pip install -e .

</p>
</details>

<details><summary>Option 2: pip</summary>
<p>

    pip install git+https://github.com/perrin-isir/xomx

</p>
</details>

-----
## Tutorials

Tutorials are the best way to learn how to use
*xomx*.

The xomx-tutorials repository contains a list of tutorials (colab notebooks) for xomx:  
https://github.com/perrin-isir/xomx-tutorials

-----
## Acknowledgements

Maintainer and main contributor:
- Nicolas Perrin-Gilbert (CNRS, ISIR)

Other people who contributed to *xomx*:
- Joshua J. Waterfall (Curie Institute)
- Julien Vibert (Curie Institute)
- Mathias Vandenbogaert (Curie Institute)
- Paul Klein (Curie Institute)

-----
## Citing the project
To cite this repository in publications:

```bibtex
@misc{xomx,
  author = {Perrin-Gilbert, Nicolas and Vibert, Julien and Vandenbogaert, Mathias and Waterfall, Joshua J.},
  title = {xomx},
  year = {2021},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/perrin-isir/xomx}},
}
```
