spatialDE

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spatialDE.

R wrapper for SpatialDE

Bioconductor version: 3.16

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 "4.2") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Software, Transcriptomics

Version 1.4.3

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License MIT + file LICENSE

Depends R (>= 4.1)

Imports reticulate, basilisk(>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, S4Vectors, 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

Suggests knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)

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Package Archives

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

Source Package spatialDE_1.4.3.tar.gz

Windows Binary spatialDE_1.4.3.zip

macOS Binary (x86_64) spatialDE_1.4.3.tgz

macOS Binary (arm64)

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

Old Source Packages for BioC 3.16 Source Archive