spatialDE

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

R wrapper for SpatialDE

Bioconductor version: Development (3.21)

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] (ORCID: ), Milan Malfait [aut] (ORCID: ), Lambda Moses [aut] (ORCID: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software, Transcriptomics
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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

Suggests	knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	spatialDE_1.13.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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