DOI: 10.18129/B9.bioc.SpatialExperiment    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see SpatialExperiment.

S4 Class for Spatial Experiments handling

Bioconductor version: 3.14

Defines S4 classes for storing data for spatial experiments. Main examples are reported by using seqFISH and 10x-Visium Spatial Gene Expression data. This includes specialized methods for storing, retrieving spatial coordinates, 10x dedicated parameters and their handling.

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

Maintainer: Dario Righelli <dario.righelli at>

Citation (from within R, enter citation("SpatialExperiment")):


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HTML R Script Introduction to the SpatialExperiment class
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (1.5 years)
License GPL-3
Depends methods, SingleCellExperiment
Imports BiocFileCache, DropletUtils, rjson, magick, grDevices, S4Vectors, SummarizedExperiment, BiocGenerics, utils
Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
Depends On Me ExperimentSubset, imcRtools, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData
Imports Me ggspavis, SingleCellMultiModal, spatialDE
Suggests Me mistyR
Links To Me
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Source Package SpatialExperiment_1.4.0.tar.gz
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