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spatialDE

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

R wrapper for SpatialDE


Bioconductor version: Development (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 unipd.it>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("spatialDE")

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

Documentation

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

browseVignettes("spatialDE")
Introduction to spatialDE HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Software, Transcriptomics
Version 1.9.1
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
System Requirements
URL https://github.com/sales-lab/spatialDE https://bioconductor.org/packages/spatialDE/
Bug Reports https://github.com/sales-lab/spatialDE/issues
See More
Suggests knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spatialDE_1.9.1.tar.gz
Windows Binary spatialDE_1.9.1.zip
macOS Binary (x86_64) spatialDE_1.9.1.tgz
macOS Binary (arm64) spatialDE_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/spatialDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialDE
Bioc Package Browser https://code.bioconductor.org/browse/spatialDE/
Package Short Url https://bioconductor.org/packages/spatialDE/
Package Downloads Report Download Stats