Metadata-Version: 2.1
Name: scatrex
Version: 0.2.0
Summary: Map single-cell transcriptomes to copy number evolutionary trees.
Home-page: https://github.com/cbg-ethz/SCATrEx
License: GNU GENERAL PUBLIC LICENSE 3
Author: pedrofale
Author-email: pedro.miguel.ferreira.pf@gmail.com
Requires-Python: >=3.7.1,<3.10
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Dist: anndata (>=0.7.5,<0.8.0)
Requires-Dist: graphviz (>=0.14.1,<0.15.0)
Requires-Dist: gseapy (>=0.10.5,<0.11.0)
Requires-Dist: jax (==0.2.20)
Requires-Dist: jaxlib (==0.1.71)
Requires-Dist: networkx (>=2.6.2,<3.0.0)
Requires-Dist: numpy (>=1.21.2,<2.0.0)
Requires-Dist: pandas (>=1.3.2,<2.0.0)
Requires-Dist: pybiomart (>=0.2.0,<0.3.0)
Requires-Dist: pygraphviz (>=1.7,<2.0)
Requires-Dist: scanpy (>=1.7.0,<2.0.0)
Requires-Dist: scikit-learn (>=0.23.2,<0.24.0)
Requires-Dist: scipy (>=1.7.3,<2.0.0)
Requires-Dist: tqdm (>=4.57.0,<5.0.0)
Project-URL: Repository, https://github.com/cbg-ethz/SCATrEx
Description-Content-Type: text/markdown

<div align="left">
  <img src="https://github.com/cbg-ethz/SCATrEx/raw/main/figures/scatrex.png", width="300px">
</div>
<p></p>

[![PyPI](https://img.shields.io/pypi/v/scatrex.svg?style=flat)](https://pypi.python.org/pypi/scatrex)
[![Build](https://github.com/cbg-ethz/SCATrEx/actions/workflows/main.yaml/badge.svg)](https://github.com/cbg-ethz/SCATrEx/actions/workflows/main.yaml)


Map single-cell transcriptomes to copy number evolutionary trees. Check out the [tutorial](https://github.com/cbg-ethz/SCATrEx/blob/main/notebooks/tutorial.ipynb) for more information.

## Installation
```
$ pip install scatrex
```

SCATrEx uses [JAX](https://github.com/google/jax) to perform automatic differentiation. By default, SCATrEx installs the CPU-only version of JAX, but we strongly recommend the use of GPU acceleration. Please follow the instructions in https://github.com/google/jax#pip-installation-gpu-cuda to install the GPU version of JAX.

## Preprint
https://doi.org/10.1101/2021.11.04.467244

