Metadata-Version: 2.1
Name: scegot
Version: 0.1.2
Summary: single cell trajectory inference framework based on Entropic Gaussian mixture Optimal Transport
Home-page: https://yachimura-lab.github.io/scEGOT/
License: MIT
Author: Toshiaki Yachimura
Author-email: toshiaki.yachimura.a4@tohoku.ac.jp
Requires-Python: >=3.9,<3.12
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: POT (>=0.9.0,<0.10.0)
Requires-Dist: anndata (==0.8)
Requires-Dist: cellmap (>=1.0.2,<2.0.0)
Requires-Dist: graphviz (>=0.20.1,<0.21.0)
Requires-Dist: ipython (>=8.14.0,<9.0.0)
Requires-Dist: jupyterlab (>=4.0.4,<5.0.0)
Requires-Dist: kaleido (==0.2.1)
Requires-Dist: llvmlite (>=0.40.1,<0.41.0)
Requires-Dist: matplotlib (<3.8.0)
Requires-Dist: natsort (>=8.4.0,<9.0.0)
Requires-Dist: networkx (>=3.1,<4.0)
Requires-Dist: pandas (>=2.0.3,<3.0.0)
Requires-Dist: plotly (>=5.15.0,<6.0.0)
Requires-Dist: pydotplus (>=2.0.2,<3.0.0)
Requires-Dist: scikit-learn (>=1.3.0,<2.0.0)
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Requires-Dist: seaborn (>=0.12.2,<0.13.0)
Requires-Dist: tqdm (>=4.65.0,<5.0.0)
Requires-Dist: umap-learn (>=0.5.3,<0.6.0)
Project-URL: Documentation, https://yachimura-lab.github.io/scEGOT/tutorial.html
Project-URL: Repository, https://github.com/yachimura-lab/scEGOT
Description-Content-Type: text/markdown

# scEGOT

single cell trajectory inference framework based on Entropic Gaussian mixture Optimal Transport

![Fig_scEGOT_abstract](https://github.com/yachimura-lab/scEGOT/assets/87163501/83a42b90-6cb4-402a-87d0-65815c44962c)

## Installation

```sh
$ pip install scegot
```

## Requirements

- Python3
- pandas
- anndata
- GraphViz

  Click [here](https://graphviz.org/) to learn how to install GraphViz (official documentation).

## Documentation

The tutorial is available [here](https://yachimura-lab.github.io/scEGOT/).

## Paper

Please see the following paper:
[Toshiaki Yachimura, Hanbo Wang, Yusuke Imoto, Momoko Yoshida, Sohei Tasaki, Yoji Kojima, Yukihiro Yabuta, Mitinori Saitou, Yasuaki Hiraoka. scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport. bioRxiv](https://doi.org/10.1101/2023.09.11.557102)

