DOI: 10.18129/B9.bioc.SpatialExperiment  

S4 Class for Spatially Resolved -omics Data

Bioconductor version: Release (3.17)

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment 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.

Author: Dario Righelli [aut, cre], Davide Risso [aut], Helena L. Crowell [aut], Lukas M. Weber [aut]

Maintainer: Dario Righelli <dario.righelli at>

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HTML R Script Introduction to the SpatialExperiment class
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biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends methods, SingleCellExperiment
Imports rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, DropletUtils, BiocGenerics, BiocFileCache
Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
Depends On Me alabaster.spatial, ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata
Imports Me CTSV, cytomapper, DESpace, escheR, ggspavis, lisaClust, MoleculeExperiment, nnSVG, scFeatures, SingleCellMultiModal, spaSim, spatialDE, SpatialFeatureExperiment, spicyR, SpotClean, standR, Statial, stJoincount, Voyager
Suggests Me GeomxTools, SPOTlight
Links To Me
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