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

R wrapper for SpatialDE

Bioconductor version: Development (3.20)

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

Author: Davide Corso [aut] , Milan Malfait [aut] , Lambda Moses [aut] , Gabriele Sales [cre]

Maintainer: Gabriele Sales <gabriele.sales at>

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


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 spatialDE HTML R Script
Reference Manual PDF


biocViews Software, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.3)
Imports reticulate, basilisk(>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra
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Suggests knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package spatialDE_1.11.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) spatialDE_1.11.0.tgz
macOS Binary (arm64) spatialDE_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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