SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

Sun, Y. H.; Piya, S.; Ouyang, Z.; Chen, Y.; Gagnon, J.; Cao, S.; Zhang, H.; Song, B.; Zhu, J.; Chandratre, K.; Yu, H.; Hu, W.; Ryals, M.; Casey, F.; Huh, D.; Zhang, B.

doi:10.1101/2025.09.15.676389

bioRxiv · 10.1101/2025.09.15.676389

SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

Sun, Y. H.·Piya, S.·Ouyang, Z.·Chen, Y.·Gagnon, J.·Cao, S.·Zhang, H.·Song, B.·Zhu, J.·Chandratre, K.·Yu, H.·Hu, W.·Ryals, M.·Casey, F.·Huh, D.·Zhang, B.

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Abstract

BackgroundSpatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the field have resulted in a variety of new platforms, including Visium, Visium HD, and Xenium from 10x Genomics, as well as GeoMx and CosMx from NanoString Technologies, which has now been acquired by the Bruker Corporation. However, the existence of diverse spatial transcriptomics platforms and various data formats poses challenges in standardizing data analysis. Thus, there remains a critical gap in the availability of a comprehensive pipeline capable of conducting end-to-end analysis that is necessary to extract biological insights from multiple spatial transcriptomics platforms. ResultsHere, we present SpaceSequest, a tailored pipeline that utilizes cutting-edge computational methodologies to conduct a thorough analysis, enabling the extraction of crucial biological insights from five major spatial transcriptomics technologies. SpaceSequest performs (1) standardized quality control and general data processing, (2) key analyses customized for each spatial platform, (3) automated cell type annotation and deconvolution, and (4) high-quality figure and analysis result generation. In addition, SpaceSequest allows for smooth integration with cellxgene VIP and Quickomics for user-friendly data access and interactive visualization. ConclusionsSpaceSequest is a unified and comprehensive pipeline designed for the analysis, visualization, and publication of spatial transcriptomics data from various platforms. The source code is available at https://github.com/interactivereport/SpaceSequest. To facilitate seamless installation and usage, we have also created a detailed Bookdown tutorial that can be accessed through https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html.

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Sun, Y. H., Piya, S., Ouyang, Z., Chen, Y., Gagnon, J., Cao, S., Zhang, H., Song, B., Zhu, J., Chandratre, K., Yu, H., Hu, W., Ryals, M., Casey, F., Huh, D., Zhang, B.. 2025-09-23. SpaceSequest: A unified pipeline for spatial transcriptomics data analysis. https://doi.org/10.1101/2025.09.15.676389

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