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.
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")
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.