pytometry: Flow & mass cytometry analytics

pytometry: Flow & mass cytometry analytics#

Tests Documentation

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

Installation#

You need to have Python 3.11 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

  1. Install the latest development version:

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

  1. Install locally for development:

Please refer to the Contributing Guide.

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.

pytometry is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

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