Cytometry Python Packages

flowio

A Python library for reading and writing Flow Cytometry Standard (FCS) files

flowutils

FlowUtils is a Python package containing various utility functions related to flow cytometry analysis, primarily focused on compensation and transformation tasks commonly used within the flow community.

flowkit

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

scyan

Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

shapeout

Shape-Out has been superseded by Shape-Out 2.

add-labels-to-fcs

This repository includes code for adding data labels to FCS files as additional data channels. It also adds labels a grid that can be gated in standard flow cytometry software.

chronoclust

A clustering algorithm that will perform clustering on each of a time-series of discrete datasets, and explicitly track the evolution of clusters over time.

cycombinepy

Python port of cyCombine: batch correction of single-cell cytometry data