TY - JOUR
T1 - STExplore
T2 - An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data
AU - Wang, Yongtian
AU - Luo, Jintian
AU - Jiao, Shaoqing
AU - Xie, Xiaohan
AU - Wang, Tao
AU - Liu, Jie
AU - Shang, Xuequn
AU - Peng, Jiajie
N1 - Publisher Copyright:
© 2025 Wiley-VCH GmbH.
PY - 2025/5/17
Y1 - 2025/5/17
N2 - Spatial transcriptomics revolutionizes the understanding of tissue organization and cellular interactions by combining high-resolution spatial information with gene expression profiles. Existing spatial transcriptomics analysis platforms face challenges in accommodating diverse techniques, integrating multi-omics data, and providing comprehensive analytical workflows. STExplore, an advanced online platform, is developed to address these limitations. STExplore supports a wide range of technologies, including sequencing-based and image-based methods, and offers a complete analysis workflow encompassing preprocessing, integration with single-cell RNA sequencing (scRNA-seq), cluster-level and gene-level analyses, and cell–cell communication studies. The platform features dynamic parameter adjustments and interactive visualizations at each analytical stage, enabling users to gain deeper insights into the spatial transcriptomic landscape. Case studies on neurogenesis in embryonic brain development, Alzheimer's disease, and brain tissue architecture demonstrate STExplore's capabilities in enhancing gene expression analysis, revealing cellular spatial organizations, and uncovering intercellular communication patterns. STExplore provides a comprehensive and user-friendly solution for the expanding demands of spatial transcriptomics research. The platform is accessible at http://120.77.47.2:3000/.
AB - Spatial transcriptomics revolutionizes the understanding of tissue organization and cellular interactions by combining high-resolution spatial information with gene expression profiles. Existing spatial transcriptomics analysis platforms face challenges in accommodating diverse techniques, integrating multi-omics data, and providing comprehensive analytical workflows. STExplore, an advanced online platform, is developed to address these limitations. STExplore supports a wide range of technologies, including sequencing-based and image-based methods, and offers a complete analysis workflow encompassing preprocessing, integration with single-cell RNA sequencing (scRNA-seq), cluster-level and gene-level analyses, and cell–cell communication studies. The platform features dynamic parameter adjustments and interactive visualizations at each analytical stage, enabling users to gain deeper insights into the spatial transcriptomic landscape. Case studies on neurogenesis in embryonic brain development, Alzheimer's disease, and brain tissue architecture demonstrate STExplore's capabilities in enhancing gene expression analysis, revealing cellular spatial organizations, and uncovering intercellular communication patterns. STExplore provides a comprehensive and user-friendly solution for the expanding demands of spatial transcriptomics research. The platform is accessible at http://120.77.47.2:3000/.
KW - data analysis
KW - interactive visualization
KW - single-cell RNA sequencing
KW - spatial transcriptomics
KW - web server
UR - http://www.scopus.com/inward/record.url?scp=86000289374&partnerID=8YFLogxK
U2 - 10.1002/smtd.202401272
DO - 10.1002/smtd.202401272
M3 - 文章
AN - SCOPUS:86000289374
SN - 2366-9608
VL - 9
JO - Small Methods
JF - Small Methods
IS - 5
M1 - 2401272
ER -