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This is the development version of SpatialFeatureExperiment; for the stable release version, see SpatialFeatureExperiment.

Integrating SpatialExperiment with Simple Features in sf

Bioconductor version: Development (3.20)

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

Author: Lambda Moses [aut, cre] , Alik Huseynov [aut] , Lior Pachter [aut, ths]

Maintainer: Lambda Moses <dlu2 at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the SpatialFeatureExperiment class HTML R Script
Reference Manual PDF


biocViews DataRepresentation, Software, Spatial, Transcriptomics
Version 1.7.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot
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Suggests arrow, BiocStyle, knitr, RBioFormats, rhdf5, rmarkdown, sfarrow, SFEData(>= 1.5.3), testthat (>= 3.0.0), Voyager, xml2, scater, Seurat, SeuratObject, dplyr, tidyr
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Depends On Me Voyager
Imports Me TENxXeniumData
Suggests Me SFEData
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Follow Installation instructions to use this package in your R session.

Source Package SpatialFeatureExperiment_1.7.0.tar.gz
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