The paper introduces SpaceSequest, a comprehensive and unified computational pipeline designed for the analysis and visualization of spatial transcriptomics data. This tool addresses the challenge of diverse data formats and platforms—such as Visium, Xenium, GeoMx, and CosMx—by offering standardized processing, quality control, customized platform-specific analyses, and automated cell type deconvolution. The paper details the implementation of SpaceSequest, showcasing its ability to perform crucial analyses like clustering with tools like BayesSpace and cell type deconvolution using Tangram and Cell2location. Overall, SpaceSequest is presented as a user-friendly, end-to-end solution aimed at facilitating the extraction of biological insights from various spatial transcriptomics technologies and generating standardized, publication-ready results.

References:

• Sun, Yu H., et al. "SpaceSequest: A unified pipeline for spatial transcriptomics data analysis." bioRxiv (2025): 2025-09.