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Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data

SODB is a large-scale platform providing rich data resources, efficient data exporting, and interactive analytical modules for spatial omics research.

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Fig. 1: Examples of visualizations using the SOView tool in SODB.


  1. Lewis, S. M. et al. Spatial omics and multiplexed imaging to explore cancer biology. Nat. Methods 18, 997–1012 (2021). This review article surveys spatial omics technologies and applications.

    Article  CAS  PubMed  Google Scholar 

  2. Wolf, F. A. et al. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018). This paper describes SCANPY, one of the most useful single-cell analysis packages.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Palla, G. et al. Squidpy: a scalable framework for spatial omics analysis. Nat. Methods 19, 171–178 (2022). This paper describes Squidpy, one of the most useful spatial omics analysis packages.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Luecken, M. D. et al. Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41–50 (2022). This paper surveys and benchmarks many computational methods for single-cell data integration.

    Article  CAS  PubMed  Google Scholar 

  5. Zeira, R. et al. Alignment and integration of spatial transcriptomics data. Nat. Methods 19, 567–575 (2022). This paper presents PASTE, a method for alignment and integration of multiple spatial transcriptomics datasets.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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This is a summary of: Yuan, Z. et al. SODB facilitates comprehensive exploration of spatial omics data. Nat. Methods (2023).

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Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data. Nat Methods 20, 359–360 (2023).

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