https://github.com/scverse/pytometry
Flow & mass cytometry analytics.
https://github.com/scverse/pytometry
Last synced: 11 months ago
JSON representation
Flow & mass cytometry analytics.
- Host: GitHub
- URL: https://github.com/scverse/pytometry
- Owner: scverse
- License: apache-2.0
- Created: 2022-07-07T12:31:29.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2025-06-23T17:35:34.000Z (12 months ago)
- Last Synced: 2025-06-23T18:40:14.370Z (12 months ago)
- Language: Python
- Homepage: https://pytometry.readthedocs.io/en/latest/index.html
- Size: 2.75 MB
- Stars: 52
- Watchers: 5
- Forks: 10
- Open Issues: 14
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# pytometry: Flow & mass cytometry analytics
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/pytometry/test.yaml?branch=main
[link-tests]: https://github.com/scverse/pytometry/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/pytometry
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-singlecell](https://rapids-singlecell.readthedocs.io/)
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api].
## Installation
You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install pytometry:
1. Install the latest release of `pytometry` from [PyPI][link-pypi].
```bash
pip install pytometry
```
2. Install the latest development version:
```bash
pip install git+https://github.com/scverse/pytometry.git@main
```
## Release notes
See [GitHub releases][changelog].
## Contact
For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].
## Citation
Pytometry is currently a pre-print on [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.10.10.511546v1).
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/scverse/pytometry/issues
[changelog]: https://github.com/scverse/pytometry/releases
[link-docs]: https://pytometry.readthedocs.io
[link-api]: https://pytometry.readthedocs.io/latest/api.html
[link-pypi]: https://pypi.org/project/pytometry
[//]: # "numfocus-fiscal-sponsor-attribution"
pytometry is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
