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

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-03-29 DOI:10.1186/s13059-025-03550-5

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

引用次数: 0

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.

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SOAPy：一个Python包，用于剖析空间架构、动态和通信

空间组学的进步使我们能够更深入地了解组织微环境，同时也带来了计算方面的挑战。因此，我们开发了一个空间组学数据的综合分析工具SOAPy，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可以应用于多种空间组学技术和生理病理背景下的多个领域，如肿瘤生物学和发育生物学。它的多功能性和强大的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不同的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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