spatialDE

DOI: 10.18129/B9.bioc.spatialDE  

R wrapper for SpatialDE

Bioconductor version: Release (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>

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")

 

HTML	R Script	Introduction to spatialDE
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Software, Transcriptomics
Version	1.4.3
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 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
LinkingTo
Suggests	knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/sales-lab/spatialDE https://bioconductor.org/packages/spatialDE/
BugReports	https://github.com/sales-lab/spatialDE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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