dbverse scales spatial omics analysis with embedded analytical databases

<jats:p>Spatial omics datasets are increasing in size and complexity, exceeding the memory of standard computers and thereby limiting data analysis. Here we present dbverse, a framework for larger-than memory matrix, spatial and genomic data analysis in embedded analytical databases. Benchmarks show dbverse provides orders of magnitude runtime improvements relative to established in-memory and file backed methods for core operations in single-cell and spatial omics analysis. We integrated dbverse with Giotto Suite, scaling end-to-end preprocessing of millions of cells and enabling spatial alternative polyadenylation analysis as demonstrated on a Visium HD 3′ ovarian clear cell carcinoma sample. The dbverse framework provides an interoperable database foundation for larger-than-memory spatial omics analysis on ordinary computers.</jats:p>