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bioRxiv · 10.1101/2021.12.24.474131

PyLiger: Scalable single-cell multi-omic data integration in Python

Lu, L.·Welch, J. D.
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Abstract

MotivationLIGER is a widely-used R package for single-cell multi-omic data integration. However, many users prefer to analyze their single-cell datasets in Python, which offers an attractive syntax and highly-optimized scientific computing libraries for increased efficiency. ResultsWe developed PyLiger, a Python package for integrating single-cell multi-omic datasets. PyLiger offers faster performance than the previous R implementation (2-5x speedup), interoperability with AnnData format, flexible on-disk or in-memory analysis capability, and new functionality for gene ontology enrichment analysis. The on-disk capability enables analysis of arbitrarily large single-cell datasets using fixed memory. AvailabilityPyLiger is available on Github at https://github.com/welch-lab/pyliger and on the Python Package Index. Contactwelchjd@umich.edu Supplementary informationSupplementary data are available at Bioinformatics online.

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Lu, L., Welch, J. D.. 2021-12-27. PyLiger: Scalable single-cell multi-omic data integration in Python. https://doi.org/10.1101/2021.12.24.474131

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