Metadata-Version: 2.1
Name: CytoSimplex
Version: 0.1.0
Summary: Simplex Visualization of Cell Fate Similarity in Single-Cell Data
Author: Yichen Wang, Jialin Liu, Joshua D. Welch
Maintainer-email: Yichen Wang <wayichen@umich.edu>
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3.10
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Dist: scikit-learn
Requires-Dist: numpy
Requires-Dist: anndata
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: mpltern
Requires-Dist: scanpy
Requires-Dist: sphinx>=4.4,<5 ; extra == "doc"
Requires-Dist: sphinx-book-theme ; extra == "doc"
Requires-Dist: sphinx_design ; extra == "doc"
Requires-Dist: scanpydoc>=0.9.5 ; extra == "doc"
Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
Requires-Dist: myst-parser ; extra == "doc"
Requires-Dist: myst-nb ; extra == "doc"
Requires-Dist: sphinx-design ; extra == "doc"
Requires-Dist: sphinxext-opengraph ; extra == "doc"
Requires-Dist: sphinx-copybutton ; extra == "doc"
Requires-Dist: nbsphinx ; extra == "doc"
Requires-Dist: matplotlib!=3.6.1 ; extra == "doc"
Requires-Dist: CytoSimplex[test-min] ; extra == "test"
Requires-Dist: pytest>=4.4 ; extra == "test-min"
Requires-Dist: pytest-nunit ; extra == "test-min"
Requires-Dist: pytest-mock ; extra == "test-min"
Project-URL: Documentation, https://cytosimplex.readthedocs.io/en/latest/
Project-URL: Source, https://github.com/welch-lab/pyCytoSimplex
Provides-Extra: doc
Provides-Extra: test
Provides-Extra: test-min

<img src="docs/images/logo_bright.png" align="right" width="120" />

# CytoSimplex

[![Python3_10_test](https://github.com/welch-lab/pyCytoSimplex/actions/workflows/python-package.yml/badge.svg)](https://github.com/welch-lab/pyCytoSimplex/actions/workflows/python-package.yml)[![codecov](https://codecov.io/gh/mvfki/pyCytoSimplex/branch/main/graph/badge.svg?token=L839lYPVon)](https://codecov.io/gh/mvfki/pyCytoSimplex)[![AnnData-0.9.1](https://img.shields.io/badge/AnnData-0.9.1-blue)](https://pypi.org/project/anndata/)

"CytoSimplex" is a Python module that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells.
RNA velocity can be added as another layer of information.

For R users, we have an R package [CytoSimplex](https://github.com/welch-lab/CytoSimplex) that provides the same functionalities.

We have build a [documentation website](https://pycytosimplex.readthedocs.io/en/latest/index.html) for:
- [Detailed instruction for installation](https://pycytosimplex.readthedocs.io/en/latest/installation.html)
- [Walkthrough example from loading data to creating different simplex visualization](https://pycytosimplex.readthedocs.io/en/latest/example/index.html)

