Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment

Lambda Moses; Alik Huseynov; Joseph Matthew Rich; Lior S. Pachter

doi:10.1101/2025.02.24.640007

BioinformaticsbioRxivFeb 24, 2025

Preprint

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment

Lambda Moses iD, Alik Huseynov iD, Joseph Matthew Rich iD, Lior S. Pachter iD

Abstract

SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data. SpatialFeatureExperiment can be used to store and analyze a variety of spatial -omics data types, including data from the Visium, Xenium, MERFISH, SeqFish, and Slide-seq platforms, bringing spatial operations to the SingleCellExperiment ecosystem.

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