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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Exner et al. (2024) studied this question.
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