One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data.

Journal: Genome biology
Published Date: Apr 20, 2022

Abstract

Integrative analysis of large-scale single-cell RNA sequencing (scRNA-seq) datasets can aggregate complementary biological information from different datasets. However, most existing methods fail to efficiently integrate multiple large-scale scRNA-seq datasets. We propose OCAT, One Cell At a Time, a machine learning method that sparsely encodes single-cell gene expression to integrate data from multiple sources without highly variable gene selection or explicit batch effect correction. We demonstrate that OCAT efficiently integrates multiple scRNA-seq datasets and achieves the state-of-the-art performance in cell type clustering, especially in challenging scenarios of non-overlapping cell types. In addition, OCAT can efficaciously facilitate a variety of downstream analyses.

Authors

  • Chloe X Wang
    University Health Network, Toronto, Canada.
  • Lin Zhang
    Laboratory of Molecular Translational Medicine, Centre for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Clinical Research Center for Birth Defects of Sichuan Province, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. Electronic address: zhanglin@scu.edu.cn.
  • Bo Wang
    Department of Clinical Laboratory Medicine Center, Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, China.

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