Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis
Our study provides a comprehensive benchmark of 12 multi-slice integration methods across four key tasks using 19 diverse datasets. Our results reveal that method performance is highly dependent on application context, dataset size, and technology. We also identified strong interdependencies between upstream and downstream tasks, highlighting the importance of robust early-stage analysis.
Authors
- Qi Liu (ORCID: https://orcid.org/0000-0002-0596-5579)
- Kejing Dong (ORCID: https://orcid.org/0009-0004-2805-4438)
- Fangliangzi Meng
- Yicheng Gao (ORCID: https://orcid.org/0009-0004-2462-5459)
- Guohui Chuai (ORCID: https://orcid.org/0000-0003-2423-8411)
- Qi Zou (ORCID: https://orcid.org/0000-0002-8662-5874)
- Zhiyuan Yuan (ORCID: https://orcid.org/0000-0002-9367-4236)
- Chen Zhang (ORCID: https://orcid.org/0000-0002-6592-9318)
- Yan Cui (ORCID: https://orcid.org/0000-0002-6833-5611)
- Chen Tang (ORCID: https://orcid.org/0000-0001-7010-2203)
- Xiaohan Chen (ORCID: https://orcid.org/0000-0001-6462-4216)
- Zhikang Wang (ORCID: https://orcid.org/0000-0001-9587-1965)
- Xiaojie Cheng
- Xuan Jin
- Senlin Lin (ORCID: https://orcid.org/0009-0001-6593-4088)
- Jingya Yang
- C.S. Han
- Shuguang Wang (ORCID: https://orcid.org/0000-0001-8072-7784)
Institutions
- Tongji University (CN)
- Fudan University (CN)
- Intelligent Systems Research (United States) (US)
- Shanghai East Hospital (CN)
- Autonomous Healthcare (US)
- Tongji Hospital (CN)
- Shanghai Center for Brain Science and Brain-Inspired Technology (CN)
- Institute of Science and Technology
Publication Details
- Journal
- Genome biology
- Published
- 2025-09-29
- DOI
- https://doi.org/10.1186/s13059-025-03796-z
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Natural Science Foundation of China
- Shanghai Education Development Foundation
- Shanghai Municipal Education Commission
- Science and Technology Commission of Shanghai Municipality
- National Key Research and Development Program of China
- Fundamental Research Funds for the Central Universities