SOAPy：一个用于剖析空间架构、动态变化和通信的Python软件包。

SOAPy: a Python package to dissect spatial architecture, dynamics, and communication.

作者信息

Wang Heqi, Li Jiarong, Jing Siyu, Lin Ping, Qiu Yiling, Yan Xi, Yuan Jiao, Tang ZhiXuan, Li Yu, Zhang Haibing, Chen Yujie, Wang Zhen, Li Hong

机构信息

CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

出版信息

Genome Biol. 2025 Mar 29;26(1):80. doi: 10.1186/s13059-025-03550-5.

DOI:10.1186/s13059-025-03550-5

PMID:40158115

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11954224/

Abstract

Advances in spatial omics enable deeper insights into tissue microenvironments while posing computational challenges. Therefore, we developed SOAPy, a comprehensive tool for analyzing spatial omics data, which offers methods for spatial domain identification, spatial expression tendency, spatiotemporal expression pattern, cellular co-localization, multi-cellular niches, cell-cell communication, and so on. SOAPy can be applied to diverse spatial omics technologies and multiple areas in physiological and pathological contexts, such as tumor biology and developmental biology. Its versatility and robust performance make it a universal platform for spatial omics analysis, providing diverse insights into the dynamics and architecture of tissue microenvironments.

摘要

空间组学的进展使我们能够更深入地了解组织微环境，但同时也带来了计算方面的挑战。因此，我们开发了SOAPy，这是一个用于分析空间组学数据的综合工具，它提供了空间域识别、空间表达趋势、时空表达模式、细胞共定位、多细胞生态位、细胞间通讯等方法。SOAPy可应用于多种空间组学技术以及生理和病理背景下的多个领域，如肿瘤生物学和发育生物学。其多功能性和强大性能使其成为空间组学分析的通用平台，为组织微环境的动态和结构提供了多样的见解。