Journal
NATURE BIOTECHNOLOGY
Volume 40, Issue 10, Pages 1458-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41587-022-01284-4
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Funding
- National Key Research and Development Program [2016YFC0901603]
- State Key Laboratory of Protein and Plant Gene Research
- Beijing Advanced Innovation Center for Genomics at Peking University
- Changping Laboratory
- National Program for Support of Top-notch Young Professionals
- High-performance Computing Platform of Peking University
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GLUE is a computational framework that bridges the gap between different omics layers by modeling regulatory interactions, and it outperforms state-of-the-art tools in accuracy, robustness, and scalability for heterogeneous single-cell multi-omics data. It has been successfully applied in various challenging tasks.
Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that different omics layers typically have distinct feature spaces. Here, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic benchmarking demonstrated that GLUE is more accurate, robust and scalable than state-of-the-art tools for heterogeneous single-cell multi-omics data. We applied GLUE to various challenging tasks, including triple-omics integration, integrative regulatory inference and multi-omics human cell atlas construction over millions of cells, where GLUE was able to correct previous annotations. GLUE features a modular design that can be flexibly extended and enhanced for new analysis tasks. The full package is available online at https://github.com/gao-lab/GLUE.
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