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

doi:10.1038/s41467-023-37168-7

	A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics
	Li, Haoyang 1,2; Zhou, Juexiao 1,2; Li, Zhongxiao 1,2; Chen, Siyuan 1,2; Liao, Xingyu 1,2; Zhang, Bin 1,2; Zhang, Ruochi 3; Wang, Yu 3; Sun, Shiwei 4,5; Gao, Xin 1,2
	2023-03-21
发表期刊	NATURE COMMUNICATIONS
卷号	14 期号:1 页码:10
摘要	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. This study comprehensively benchmarks 18 state-of-the-art methods for cellular deconvolution of spatial transcriptomics and provide decision-tree-style guidelines and recommendations for method selection.
DOI	10.1038/s41467-023-37168-7
收录类别	SCI
语种	英语
资助项目	King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[FCC/1/1976-44-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[FCC/1/1976-45-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[URF/1/4663-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[REI/1/5202-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[REI/1/5234-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[REI/1/4940-01-01] ; King Abdullah University of Science and Technology (KAUST) Office of Research Administration (ORA)[RGC/3/4816-01-01]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001001758000003
出版者	NATURE PORTFOLIO
引用统计	被引频次：19[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/21204
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Gao, Xin
作者单位	1.King Abdullah Univ Sci & Technol KAUST, Computat Biosci Res Ctr, Thuwal, Saudi Arabia 2.King Abdullah Univ Sci & Technol KAUST, Comp Elect & Math Sci & Engn Div, Thuwal, Saudi Arabia 3.Syneron Technol, Guangzhou 510000, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Li, Haoyang,Zhou, Juexiao,Li, Zhongxiao,et al. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics[J]. NATURE COMMUNICATIONS,2023,14(1):10.
APA	Li, Haoyang.,Zhou, Juexiao.,Li, Zhongxiao.,Chen, Siyuan.,Liao, Xingyu.,...&Gao, Xin.(2023).A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.NATURE COMMUNICATIONS,14(1),10.
MLA	Li, Haoyang,et al."A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics".NATURE COMMUNICATIONS 14.1(2023):10.