A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun and Xin Gao ()
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Haoyang Li: King Abdullah University of Science and Technology (KAUST)
Juexiao Zhou: King Abdullah University of Science and Technology (KAUST)
Zhongxiao Li: King Abdullah University of Science and Technology (KAUST)
Siyuan Chen: King Abdullah University of Science and Technology (KAUST)
Xingyu Liao: King Abdullah University of Science and Technology (KAUST)
Bin Zhang: King Abdullah University of Science and Technology (KAUST)
Ruochi Zhang: Syneron Technology
Yu Wang: Syneron Technology
Shiwei Sun: Chinese Academy of Sciences
Xin Gao: King Abdullah University of Science and Technology (KAUST)

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract Spatial transcriptomics technologies are used to profile transcriptomes while preserving spatial information, which enables high-resolution characterization of transcriptional patterns and reconstruction of tissue architecture. Due to the existence of low-resolution spots in recent spatial transcriptomics technologies, uncovering cellular heterogeneity is crucial for disentangling the spatial patterns of cell types, and many related methods have been proposed. Here, we benchmark 18 existing methods resolving a cellular deconvolution task with 50 real-world and simulated datasets by evaluating the accuracy, robustness, and usability of the methods. We compare these methods comprehensively using different metrics, resolutions, spatial transcriptomics technologies, spot numbers, and gene numbers. In terms of performance, CARD, Cell2location, and Tangram are the best methods for conducting the cellular deconvolution task. To refine our comparative results, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, which will help users easily choose the best method for fulfilling their concerns.

Date: 2023
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DOI: 10.1038/s41467-023-37168-7

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