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

Follow https://twitter.com/marenbuettner for updates.

For the code enthusiasts: Find our code base on Github.

Installation

You can install pytometry via pip from PyPI:

pip install pytometry

or from GitHub:

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

Updates

• May 3rd 2023: New release 0.1.5 with FlowSOM clustering and autologicle normalization.
• August 28th 2023: New release with various fixes and improvements.
• October 12th 2022: First public release announcement on Twitter

Citation

Pytometry is currently a pre-print on bioRxiv.