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bioRxiv · 10.64898/2026.08.12.744148

scDblFinder in Python with GPU support

Hiropedi, A.·Germain, P.-L.
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Abstract

High-throughput single-cell sequencing provides a scalable solution for characterizing cells and profiling gene expression for hundreds to millions of cells. However, this process gives rise to doublets, which can lead to inaccurate conclusions drawn from the data. A number of packages have therefore been developed to help accurately detect them, and in particular scDblFinder has been shown to outperform alternatives in the detection of doublets in single-cell (RNA) sequencing data. Being implemented in R, however, its adoption has been more limited in the Python community. Here, we present scDblFinderPy, a Python-based implementation of the scDblFinder R method, and show that it obtains similar performances. Furthermore, we include in it optional GPU support, thus further speeding up the process.

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Hiropedi, A., Germain, P.-L.. 2026-08-20. scDblFinder in Python with GPU support. https://doi.org/10.64898/2026.08.12.744148

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