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

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

Authors

Exner, T.; Hackert, N. S.; Leomazzi, L.; Van Gassen, S.; Saeys, Y.; Lorenz, H.-M.; Grieshaber-Bouyer, R.

Abstract

Motivation: We present a python implementation of the widely used CytoNorm algorithm for the removal of batch effects. Results Our 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 implementation: The CytoNormPy implementation is freely available on GitHub: https://github.com/TarikExner/CytoNormPy.

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