STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing.

ABSTRACT: The recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity in the spatial context. However, the current limitations of spatial technologies hamper the exploration of cellular localizations and interactions at single-cell level. Here, we present spatial transcriptomics deconvolution by topic modeling (STRIDE), a computational method to decompose cell types from spatial mixtures by leveraging topic profiles trained from single-cell transcriptomics. STRIDE accurately estimated the cell-type proportions and showed balanced specificity and sensitivity compared to existing methods. We demonstrated STRIDE's utility by applying it to different spatial platforms and biological systems. Deconvolution by STRIDE not only mapped rare

SUBMITTER: Sun D 

PROVIDER: S-EPMC9023289 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature