MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in Bioconductor.

Abstract

Imaging-based spatial transcriptomics technologies have achieved subcellular resolution, enabling detection of individual molecules in their native tissue context. Data associated with these technologies promises unprecedented opportunity towards understanding cellular and subcellular biology. However, in R/Bioconductor there is a scarcity of existing computational infrastructure to represent such data, and particularly to summarize and transform it for existing widely adopted computational tools in single cell transcriptomics analysis, including SingleCellExperiment and SpatialExperiment classes. With the emergence of several commercial offerings of imaging-based spatial transcriptomics, there is a pressing need to develop consistent data structure standards for these technologies at the individual molecule level. To this end, we have developed MoleculeExperiment, an R/Bioconductor package, which i) stores molecule and cell segmentation boundary information at the molecule-level, ii) standardises this molecule-level information across different imaging-based ST technologies, including 10x Genomics' Xenium, and iii) streamlines transition from a MoleculeExperiment object to a SpatialExperiment object. Overall, MoleculeExperiment is generally applicable as a data infrastructure class for consistent analysis of molecule-resolved spatial omics data. The MoleculeExperiment package is publicly available on Bioconductor at https://bioconductor.org/packages/release/bioc/html/MoleculeExperiment.html. Source code is available on Github at: https://github.com/SydneyBioX/MoleculeExperiment. The vignette for MoleculeExperiment can be found at https://bioconductor.org/packages/release/bioc/html/MoleculeExperiment.html. Supplementary data are available at Bioinformatics online.