Metadata-Version: 2.1
Name: elpigraph-python
Version: 0.2.8
Home-page: https://github.com/j-bac/elpigraph-python
Maintainer: Jonathan Bac
Maintainer-email: 
Project-URL: Bug Reports, https://github.com/j-bac/elpigraph-python/issues
Project-URL: Source, https://github.com/j-bac/elpigraph-python/
Keywords: machine_learning graphs dimension_reduction single_cell
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Description-Content-Type: text/markdown
Provides-Extra: tests
Provides-Extra: docs
License-File: LICENSE

[![Documentation Status](https://readthedocs.org/projects/elpigraph-python/badge/?version=latest)](https://elpigraph-python.readthedocs.io/en/latest/?badge=latest)
[![GitHub license](https://img.shields.io/github/license/j-bac/elpigraph-python)](https://github.com/j-bac/elpigraph-python/blob/master/LICENSE)
[![DOI:10.3390/e22030296](https://img.shields.io/badge/DOI-10.3390%2Fe22030296-blue)](https://doi.org/10.3390/e22030296)

Description
===========

This package provides a Python implementation of the ElPiGraph algorithm with cpu and gpu support. Usage is explained in the [documentation](https://elpigraph-python.readthedocs.io/en/latest/) and a
self-contained description of the algorithm is available
[here](https://github.com/auranic/Elastic-principal-graphs/blob/master/ElPiGraph_Methods.pdf)
or in the [paper](https://www.mdpi.com/1099-4300/22/3/296)

It replicates the [R implementation](https://github.com/j-bac/ElPiGraph.R),
coded by [Luca Albergante](https://github.com/Albluca) and should return exactly the same results. Please open an issue if you do  notice different output. Differences between the two versions are detailed in [differences.md](differences.md). This package extends initial work by [Louis Faure](https://github.com/LouisFaure/ElPiGraph.P) and [Alexis Martin](https://github.com/AlexiMartin/ElPiGraph.P).

A native MATLAB implementation of the algorithm (coded by [Andrei
Zinovyev](https://github.com/auranic/) and [Evgeny
Mirkes](https://github.com/Mirkes)) is also
[available](https://github.com/auranic/Elastic-principal-graphs)

Requirements
============

Requirements are listed in requirements.txt. In addition, to enable gpu support cupy is needed:
https://docs-cupy.chainer.org/en/stable/install.html

Installation
====================
```bash
git clone https://github.com/j-bac/elpigraph-python.git
cd elpigraph
pip install .
```
or

```bash
pip install elpigraph-python
```

Citation
========

When using this package, please cite our [paper](https://www.mdpi.com/1099-4300/22/3/296):
Albergante, L.  et al . Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph (2020)
