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Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
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Journal Article
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
2022
Overview
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
.
Different single-cell data modalities are integrated at atlas-scale by modeling regulatory interactions.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
