To address the identified limitations and provide a more comprehensive solution for spatial transcriptomics data analysis, we have developed STExplore, an advanced online platform dedicated to spatial transcriptomics. STExplore distinguishes itself through its versatility and extensive feature set, capable of accommodating a wide array of spatial transcriptomics data from all prevailing techniques, including both sequencing-based and image-based modalities. It facilitates integration with single-cell RNA sequencing (scRNA-seq) data, thereby enhancing the investigation of cellular heterogeneity and spatial correlations. The platform implements a comprehensive analytical workflow, including preprocessing, deconvolution, imputation, batch correction, dimensionality reduction, clustering, neighborhood analysis, differential gene expression analysis, spatial variable genes, enrichment analysis, single sample gene set enrichment analysis and cell-cell communication. Throughout every analytical phase, the platform delivers interactive visualizations of results, empowering users to intuitively observe and validate hypotheses.

STExplore is open and free for everyone. All the submitted spatial transcriptomics data are secured. All data will be stored on the server for 7 days. When using this web server, The number of concurrent jobs per user must not exceed 3 when using this web server.

Wang Y, Luo J, Jiao S, Xie X, Wang T, Liu J, Shang X, Peng J. STExplore: An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data. Small Methods. 2025 Mar 5:e2401272. doi: 10.1002/smtd.202401272.