Metadata-Version: 2.1
Name: pytometry
Version: 0.1.3
Summary: Pytometry is a Python package for flow and mass cytometry analysis.
Author-email: Maren Buettner <maren.buettner@helmholtz-muenchen.de>
Description-Content-Type: text/markdown
Requires-Dist: nbproject
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: anndata
Requires-Dist: scanpy
Requires-Dist: scipy
Requires-Dist: seaborn
Requires-Dist: matplotlib
Requires-Dist: readfcs
Requires-Dist: datashader
Requires-Dist: pre-commit ; extra == "dev"
Requires-Dist: nox ; extra == "dev"
Requires-Dist: lndocs==0.2.0 ; extra == "dev"
Requires-Dist: pytest>=6.0 ; extra == "test"
Requires-Dist: pytest-cov ; extra == "test"
Project-URL: Home, https://github.com/buettnerlab/pytometry
Provides-Extra: dev
Provides-Extra: test

[![pypi](https://img.shields.io/pypi/v/pytometry?color=blue&label=pypi%20package)](https://pypi.org/project/pytometry)
[![codecov](https://codecov.io/gh/buettnerlab/pytometry/branch/main/graph/badge.svg?token=AEG5ra92HV)](https://codecov.io/gh/buettnerlab/pytometry)
[![Stars](https://img.shields.io/github/stars/buettnerlab/pytometry?logo=GitHub&color=yellow)](https://github.com/buettnerlab/pytometry/stargazers)
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# Pytometry: Flow & mass cytometry analytics

This package provides efficient and scalable handling of flow and mass cytometry data analysis. It provides

- the functionality to read in flow data in the fcs file format as [anndata](https://anndata.readthedocs.io/en/latest/) objects
- flow and mass cytometry specific preprocessing tools
- access to the entire [scanpy](https://scanpy.readthedocs.io/en/stable/) workflow functionality
- GPU support through [rapids](https://github.com/clara-parabricks/rapids-single-cell-examples)

Follow [https://twitter.com/marenbuettner](https://twitter.com/marenbuettner) for updates.

For the code enthusiasts: Find our code base on [Github](https://github.com/buettnerlab/pytometry).

## Installation

You can install `pytometry` via [pip](https://pip.pypa.io/) from [PyPI](https://pypi.org/):

```
pip install pytometry
```

or from GitHub:

```
pip install git+https://github.com/buettnerlab/pytometry.git
```

## Updates

- October 12th 2022: First public release announcement on [Twitter](https://twitter.com/marenbuettner/status/1580160765201244161?s=20&t=mTBLcUaqKs9eMzEpOWnG0g)

## Citation

Pytometry is currently a pre-print on [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.10.10.511546v1).

