spatialDE

DOI: 10.18129/B9.bioc.spatialDE    

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

R wrapper for SpatialDE

Bioconductor version: Development (3.15)

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, cre] , Milan Malfait [aut] , Lambda Moses [aut]

Maintainer: Davide Corso <davide.corso.2 at phd.unipd.it>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to spatialDE
PDF   Reference Manual
Text   LICENSE

Details

biocViews Software, Transcriptomics
Version 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports reticulate, basilisk, 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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) spatialDE_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/spatialDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialDE
Package Short Url https://bioconductor.org/packages/spatialDE/
Package Downloads Report Download Stats

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