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R wrapper for SpatialDE

Bioconductor version: Release (3.19)

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))


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 1.10.0
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_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) spatialDE_1.10.0.tgz
macOS Binary (arm64) spatialDE_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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