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Author:

Yan, Yinqiao (Yan, Yinqiao.) | Luo, Xiangyu (Luo, Xiangyu.)

Indexed by:

Scopus SCIE

Abstract:

The spatial transcriptomics is a rapidly evolving biological technology that simultaneously measures the gene expression profiles and the spatial locations of spots. With progressive advances, current spatial transcriptomic techniques can achieve the cellular or even the subcellular resolution, making it possible to explore the fine-grained spatial pattern of cell types within one tissue section. However, most existing cell spatial clustering methods require a correct specification of the cell type number, which is hard to determine in the practical exploratory data analysis. To address this issue, we present a nonparametric Bayesian model BACT to perform BAyesian Cell Typing by utilizing gene expression information and spatial coordinates of cells. BACT incorporates a nonparametric Potts prior to induce neighboring cells' spatial dependency, and, more importantly, it can automatically learn the cell type number directly from the data without prespecification. Evaluations on three single-cell spatial transcriptomic datasets demonstrate the better performance of BACT than competing spatial cell typing methods. The R package and the user manual of BACT are publicly available at https://github.com/yinqiaoyan/BACT.

Keyword:

spatial pattern Bayesian inference cell typing single-cell spatial transcriptomics

Author Community:

  • [ 1 ] [Yan, Yinqiao]Beijing Univ Technol, Sch Math Stat & Mech, 100 Pingleyuan, Beijing 100124, Peoples R China
  • [ 2 ] [Luo, Xiangyu]Renmin Univ China, Inst Stat & Big Data, 59 Zhongguancun St, Beijing 100872, Peoples R China

Reprint Author's Address:

  • [Luo, Xiangyu]Renmin Univ China, Inst Stat & Big Data, 59 Zhongguancun St, Beijing 100872, Peoples R China

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Source :

BRIEFINGS IN BIOINFORMATICS

ISSN: 1467-5463

Year: 2025

Issue: 1

Volume: 26

9 . 5 0 0

JCR@2022

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count:

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 3

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