Metadata-Version: 2.1
Name: scdef
Version: 0.0.11
Summary: Extract hierarchical signatures of cell state from single-cell data.
Home-page: https://github.com/cbg-ethz/scdef
License: MIT
Author: pedrofale
Author-email: pedro.miguel.ferreira.pf@gmail.com
Requires-Python: >=3.8
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: anndata (>=0.9.1,<0.10.0)
Requires-Dist: click (>=8.0.1,<9.0.0)
Requires-Dist: graphviz (>=0.14.2,<0.15.0)
Requires-Dist: gseapy (>=1.0.4,<2.0.0)
Requires-Dist: igraph (>=0.10.4,<0.11.0)
Requires-Dist: jax (>=0.3.25,<0.4.0)
Requires-Dist: jaxlib (>=0.3.25,<0.4.0)
Requires-Dist: numpy (>=1.23.4,<2.0.0)
Requires-Dist: pandas (>=1.5.1,<2.0.0)
Requires-Dist: scanpy (>=1.9.3,<2.0.0)
Requires-Dist: tqdm (>=4.64.0,<5.0.0)
Project-URL: Repository, https://github.com/cbg-ethz/scdef
Description-Content-Type: text/markdown

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

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

Deep exponential families for single-cell data. scDEF learns *de novo* gene signatures from scRNA-seq data at multiple levels of resolution.

## Installation
```
pip install scdef
```

Please be sure to install a version of [JAX](https://jax.readthedocs.io/) that is compatible with your GPU (if applicable).

## Getting started
scDEF takes as input an [AnnData](https://anndata.readthedocs.io/) object containing UMI counts. The [notebooks](https://github.com/cbg-ethz/scDEF/tree/main/notebooks) directory contains IPython notebooks with examples showcasing the analyses enabled by scDEF.

