STExplore: An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data

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/.