SpatialExperiment

SpatialExperiment is an R/Bioconductor S4 class for storing data from spatial -omics experiments. The class extends the SingleCellExperiment class for single-cell data to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

The SpatialExperiment package is available from Bioconductor.

A vignette containing examples and documentation is available from Bioconductor, and additional details are provided in our paper.

The following schematic illustrates the SpatialExperiment class structure.

<img src="vignettes/SPE.png" width="800"/>

Installation

The current release version of the SpatialExperiment package can be installed from Bioconductor as follows. This is the recommended approach for most users.

install.packages("BiocManager")
BiocManager::install("SpatialExperiment")

The latest development version can be installed from the development version of Bioconductor or from GitHub (which may also require some dependency packages to be installed manually).

remotes::install_github("drighelli/SpatialExperiment")

Citation

Righell D.*, Weber L.M.*, Crowell H.L.*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.⁺, and Risso D.⁺ (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11), 3128-3131.