SpatioMark: quantifying the impact of spatial proximity on cell phenotype.
MOTIVATION: As research advances in spatially resolving the biological archetype of various diseases, technologies that capture the spatial relationships between cells are demonstrating increasing value. Whilst there are an increasing number of analytical methods being developed to identify the complex web of interactions between cells, the downstream impacts of these cell-cell relationships are under explored. RESULTS: We present SpatioMark, a statistical framework that simplifies the assessment of gene or protein expression changes within a cell type that are associated with the spatial proximity to other cell types. We demonstrate its performance across spatial proteomics and transcriptomics datasets. We link identified relationships with differences in patient survival. We highlight key challenges in identifying changes in molecular markers associated with the localization of cells. We propose correction strategies that reduce artefact-induced relationships. AVAILABILITY AND IMPLEMENTATION: SpatioMark is implemented in the Statial R package on Bioconductor: https://bioconductor.org/packages/release/bioc/html/Statial.html.