SOAPy: a Python package to dissect spatial architecture, dynamics, and communication
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.
Authors
- Haibing Zhang (ORCID: https://orcid.org/0000-0002-8814-7378)
- Jiarong Li (ORCID: https://orcid.org/0009-0006-0334-7757)
- Jiao Yuan (ORCID: https://orcid.org/0000-0003-2597-2319)
- Siyu Jing (ORCID: https://orcid.org/0000-0003-2910-4201)
- Heqi Wang (ORCID: https://orcid.org/0009-0000-4239-9177)
- Xi Yan (ORCID: https://orcid.org/0009-0005-6464-8230)
- Hong Li (ORCID: https://orcid.org/0000-0001-5679-9980)
- Yu Li (ORCID: https://orcid.org/0000-0001-6910-5933)
- Zhen Wang (ORCID: https://orcid.org/0000-0001-8108-627X)
- Ping Lin (ORCID: https://orcid.org/0000-0003-3194-5595)
- Yiling Qiu
- Yujie Chen (ORCID: https://orcid.org/0009-0006-4545-7313)
- Z.G. Tang
Institutions
- Shanghai Institute of Nutrition and Health (CN)
- University of Chinese Academy of Sciences (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2025-03-29
- DOI
- https://doi.org/10.1186/s13059-025-03550-5
- Citations
- 10
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 8.06