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

Abstract

Motivation: LIGER 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. Results: We developed PyLiger, a Python package for integrating single-cell multi-omic datasets. PyLiger offers faster performance than the previous R implementation (2-5× 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.