xomx: a python library for computational omics
Project description
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 objects, which makes it fully compatible with Scanpy.
xomx is currently in beta version.
Install
Option 1: conda (preferred option)
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:
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 .
Option 2: pip
pip install xomx
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:
@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}},
}
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