CytoNormPy enables a fast and scalable removal of batch effects in cytometry datasets

Abstract

AbstractMotivationWe present a python implementation of the widely used CytoNorm algorithm for the removal of batch effects.ResultsOur implementation ran up to 85% faster than its R counterpart, while being fully compatible with common single-cell data structures and -frameworks of python. We extend the previous functionality by adding common clustering algorithms and provide key visualizations of the algorithm and its evaluation.Availability and implementationThe CytoNormPy implementation is freely available on GitHub:https://github.com/TarikExner/CytoNormPy.