spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Background: Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results: We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user's computer or through a web application. Conclusions: spatialLIBD is available at https://bioconductor.org/package/spatialLlBD . It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform.

Automated summary

This study introduces a software package that enables interactive exploration of spatial transcriptomics data generated using the Visium platform. The package allows users to analyze and understand spatially-resolved data through interactive visualization tools.