Benchmarking strategies for cross-species integration of single-cell RNA sequencing data.

ABSTRACT: The growing number of available single-cell gene expression datasets from different species creates opportunities to explore evolutionary relationships between cell types across species. Cross-species integration of single-cell RNA-sequencing data has been particularly informative in this context. However, in order to do so robustly it is essential to have rigorous benchmarking and appropriate guidelines to ensure that integration results truly reflect biology. Here, we benchmark 28 combinations of gene homology mapping methods and data integration algorithms in a variety of biological settings. We examine the capability of each strategy to perform species-mixing of known homologous cell types and to preserve biological heterogeneity using 9 established metrics. We also develop a new biolo

SUBMITTER: Song Y 

PROVIDER: S-EPMC10576752 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature