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scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.

Jinpu Li·Mauminah Raina·Yiqing Wang·Chunhui Xu·Li Su·Qi Guo·Ricardo Melo Ferreira·Michael T Eadon·Qin Ma·Juexin Wang·Dong Xu
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Abstract

MOTIVATION: Emerging spatial omics technologies empower comprehensive exploration of biological systems from multi-omics perspectives in their native tissue location in 2D and 3D space. However, the limited sequencing depth, increasing spatial resolution, and growing spatial spots in spatial omics technologies present significant computational challenges in identifying biologically meaningful molecules with variable spatial distributions across various omics modalities. RESULTS: We introduce scBSP, an open-source, versatile, and user-friendly package for identifying spatially variable features in large-scale spatial omics data. scBSP demonstrates significantly enhanced computational efficiency, processing high-resolution spatial omics data within seconds, and exhibits robust cross-platform performance by consistently identifying spatially variable features with high reproducibility across various sequencing platforms. AVAILABILITY AND IMPLEMENTATION: scBSP is available for download from R CRAN at https://cran.r-project.org/web/packages/scBSP/index.html and PyPI at https://pypi.org/project/scbsp/.

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SoftwareComputational BiologyGenomicsHumansAlgorithmsJournal ArticleResearch Support, N.I.H., Extramural

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Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T Eadon, Qin Ma, Juexin Wang, Dong Xu. 2025-10-02. scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.. https://doi.org/10.1093/bioinformatics%2Fbtaf554

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