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

IF 10.7 2区材料科学 Q1 CHEMISTRY, PHYSICAL

Small Methods Pub Date : 2025-03-05 DOI:10.1002/smtd.202401272

Yongtian Wang, Jintian Luo, Shaoqing Jiao, Xiaohan Xie, Tao Wang, Jie Liu, Xuequn Shang, Jiajie Peng

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引用次数: 0

Abstract

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/.

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STExplore：空间转录组学数据综合分析和可视化集成在线平台。

空间转录组学通过将高分辨率空间信息与基因表达谱相结合，彻底改变了对组织组织和细胞相互作用的理解。现有的空间转录组学分析平台在适应多种技术、整合多组学数据和提供全面的分析工作流程方面面临挑战。STExplore，一个先进的在线平台，就是为了解决这些限制而开发的。STExplore支持广泛的技术，包括基于测序和基于图像的方法，并提供完整的分析工作流程，包括预处理，与单细胞RNA测序（scRNA-seq）集成，集群水平和基因水平分析，以及细胞-细胞通信研究。该平台在每个分析阶段都具有动态参数调整和交互式可视化功能，使用户能够更深入地了解空间转录组景观。对胚胎脑发育、阿尔茨海默病和脑组织结构中的神经发生的案例研究表明，STExplore在增强基因表达分析、揭示细胞空间组织和揭示细胞间通信模式方面的能力。STExplore为空间转录组学研究的不断扩大的需求提供了一个全面和用户友好的解决方案。该平台可通过http://120.77.47.2:3000/访问。

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来源期刊

Small Methods Materials Science-General Materials Science

CiteScore

17.40

自引率

1.60%

发文量

347

期刊介绍： Small Methods is a multidisciplinary journal that publishes groundbreaking research on methods relevant to nano- and microscale research. It welcomes contributions from the fields of materials science, biomedical science, chemistry, and physics, showcasing the latest advancements in experimental techniques. With a notable 2022 Impact Factor of 12.4 (Journal Citation Reports, Clarivate Analytics, 2023), Small Methods is recognized for its significant impact on the scientific community. The online ISSN for Small Methods is 2366-9608.