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![alt text](https://raw.githubusercontent.com/perrin-isir/xomx/master/logo.png \"xomx logo\")\n\n![version](https://img.shields.io/badge/version-0.1.16-blue)\n[![codestyle](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Documentation](https://img.shields.io/github/actions/workflow/status/perrin-isir/xomx/docs.yml?branch=master\u0026label=docs)](https://perrin-isir.github.io/xomx/)\n[![PyPI version](https://img.shields.io/pypi/v/xomx)](https://pypi.org/project/xomx/)\n\n*xomx* is an open-source python library providing data processing and \nmachine learning tools for computational omics, with a \nparticular emphasis on explainability.\n\nIt relies on [AnnData](https://anndata.readthedocs.io) objects, which makes it\nfully compatible with [Scanpy](https://scanpy.readthedocs.io).\n\n*xomx is currently in beta version.*\n\n-----\n\n\n\n## Install\n\n\u003cdetails\u003e\u003csummary\u003eOption 1: conda (preferred option)\u003c/summary\u003e\n\u003cp\u003e\n\nThis option is preferred because it relies mainly on conda-forge  (which among other things simplifies the installation of JAX).\n\n\n    git clone https://github.com/perrin-isir/xomx.git\n    cd xomx\n    conda update conda\n    \nInstall 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):\n\n    conda install -c conda-forge micromamba\n\nChoose a conda environment name, for instance `xomxenv`.  \nThe following command creates the `xomxenv` environment with the requirements listed in [environment.yaml](environment.yaml):\n\n    micromamba create --name xomxenv --file environment.yaml\n\nIf you prefer to update an existing environment (`existing_env`):\n\n    micromamba update --name existing_env --file environment.yml\n\nThen, activate the `xomxenv` environment:\n\n    micromamba activate xomxenv\n\nFinally, to install the *xomx* library in the activated environment:\n\n    pip install -e .\n\n\u003c/p\u003e\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eOption 2: pip\u003c/summary\u003e\n\u003cp\u003e\n\nFor the pip install, you need to properly install JAX yourself. Otherwise, if JAX is installed automatically as a pip dependency of *xomx*, it will probably not work as desired (e.g. it will not be GPU-compatible). So you should install it beforehand, following these guidelines: \n\n[https://github.com/google/jax#installation](https://github.com/google/jax#installation) \n\nThen, install *xomx* with:\n\n    pip install xomx\n\n\u003c/p\u003e\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eJAX\u003c/summary\u003e\n\u003cp\u003e\n\nThe neural network-based machine learning algorithms in *xomx* are written in JAX (and flax), so it needs to be installed properly for them to work.\n\nTo verify that the JAX installation went well, check the backend used by JAX with the following command:\n```\npython -c \"import jax; print(jax.lib.xla_bridge.get_backend().platform)\"\n```\nIt will print \"cpu\", \"gpu\" or \"tpu\" depending on the platform JAX is using.\n\n\u003c/p\u003e\n\u003c/details\u003e\n\n-----\n## Tutorials\n\nTutorials are the best way to learn how to use\n*xomx*.\n\nThe xomx-tutorials repository contains a list of tutorials (colab notebooks) for xomx:  \nhttps://github.com/perrin-isir/xomx-tutorials\n\n-----\n## Acknowledgements\n\nMaintainer and main contributor:\n- Nicolas Perrin-Gilbert (CNRS, ISIR)\n\nOther people who contributed to *xomx*:\n- Joshua J. Waterfall (Curie Institute)\n- Julien Vibert (Curie Institute)\n- Mathias Vandenbogaert (Curie Institute)\n- Paul Klein (Curie Institute)\n\n-----\n## Citing the project\nTo cite this repository in publications:\n\n```bibtex\n@misc{xomx,\n  author = {Perrin-Gilbert, Nicolas and Vibert, Julien and Vandenbogaert, Mathias and Waterfall, Joshua J.},\n  title = {xomx},\n  year = {2021},\n  publisher = {GitHub},\n  journal = {GitHub repository},\n  howpublished = {\\url{https://github.com/perrin-isir/xomx}},\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fperrin-isir%2Fxomx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fperrin-isir%2Fxomx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fperrin-isir%2Fxomx/lists"}