SpatialDWLS: accurate deconvolution of spatial transcriptomic data

被引:155
作者
Dong, Rui [1 ,2 ]
Yuan, Guo-Cheng [1 ,3 ]
机构
[1] Harvard Med Sch, Dana Farber Canc Inst, Dept Pediat Oncol, Boston, MA 02215 USA
[2] Harvard Med Sch, Massachusetts Gen Hosp, Canc Ctr, Charlestown, MA 02129 USA
[3] Icahn Sch Med Mt Sinai, Charles Bronfman Inst Personalized Med, Dept Genet & Genom Sci, New York, NY 10029 USA
关键词
Spatial transcriptomics; Single cell; Deconvolution; GENE-EXPRESSION; TISSUE; SEQ;
D O I
10.1186/s13059-021-02362-7
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Recent development of spatial transcriptomic technologies has made it possible to characterize cellular heterogeneity with spatial information. However, the technology often does not have sufficient resolution to distinguish neighboring cell types. Here, we present spatialDWLS, to quantitatively estimate the cell-type composition at each spatial location. We benchmark the performance of spatialDWLS by comparing it with a number of existing deconvolution methods and find that spatialDWLS outperforms the other methods in terms of accuracy and speed. By applying spatialDWLS to a human developmental heart dataset, we observe striking spatial temporal changes of cell-type composition during development.
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页数:10
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