PyLiger: scalable single-cell multi-omic data integration in Python.

ABSTRACT:

Motivation

LIGER (Linked Inference of Genomic Experimental Relationships) 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.

Availability and

SUBMITTER: Lu L 

PROVIDER: S-EPMC9306758 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature