SpatialExperiment is an R/Bioconductor S4 class for storing data from spatially resolved transcriptomics (ST) 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 ST 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 preprint.
The SpatialExperiment package can be installed from Bioconductor. Note that Bioconductor follows a "release" and "development" schedule, where the release version is considered to be stable and updated every 6 months, and the development version contains latest updates (and then becomes the next release version every 6 months).
To install the stable release version, install the latest release version of R from CRAN, then install the Bioconductor package installer and the SpatialExperiment package as follows.
install.packages("BiocManager")
BiocManager::install("SpatialExperiment")
To install the development version, there are two options.
(i) Install the appropriate version of R (R-release between April and October, or R-devel between October and April), then install the Bioconductor package installer and the development version of the SpatialExperiment package as follows.
install.packages("BiocManager")
BiocManager::install("SpatialExperiment", version = "devel")
(ii) Alternatively, if you do not want to install R-devel (since this may cause issues with other packages), you can use the latest release version of R from CRAN and install the development version of the SpatialExperiment package from GitHub as follows.
install.packages("remotes")
remotes::install_github("drighelli/SpatialExperiment")
In version 1.5.2 (2022-01-09) the spatialData slot was deprecated, with columns previously stored in spatialData now recommended to be stored in colData. The spatialCoords slot (x and y coordinates) is unchanged. Existing objects are backward-compatible (and a console message is returned if spatialData is still used), however we recommend re-building existing objects to move the contents of spatialData to colData to ensure longer-term compatibility with any future updates.
To use version 1.5.2 or later (as of January 2022), please follow the installation instructions for the development version above.
(These updates will also be available in the release version from mid-April 2022 onwards, following the Bioconductor release schedule.)
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.+ (2021), SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor, bioRxiv.