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 objects
• flow and mass cytometry specific preprocessing tools
• access to the entire scanpy workflow functionality
• GPU support through rapids-singlecell

Getting started

Please refer to the documentation. In particular, the

• API documentation.

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.

There are several alternative options to install pytometry:

1. Install the latest release of pytometry from PyPI.

pip install pytometry

2. Install the latest development version:

pip install git+https://github.com/scverse/pytometry.git@main

Release notes

See GitHub releases.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

Pytometry is currently a pre-print on bioRxiv.