spatialDE

This is the released version of spatialDE; for the devel version, see spatialDE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

R wrapper for SpatialDE

Bioconductor version: Release (3.23)

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: 0000-0001-8845-3693 , Milan Malfait [aut] ORCID: 0000-0001-9144-3701 , Lambda Moses [aut] ORCID: 0000-0002-7092-9427 , Gabriele Sales [cre]

Maintainer: Gabriele Sales <gabriele.sales at unipd.it>

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

Davide Corso, Milan Malfait, Lambda Moses. spatialDE: R wrapper for SpatialDE. doi:10.18129/B9.bioc.spatialDE, R package version 1.18.0, https://bioconductor.org/packages/spatialDE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (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

Suggests	knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	spatialDE_1.18.0.tar.gz
Windows Binary (x86_64)	spatialDE_1.18.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	spatialDE_1.18.0.tgz
macOS Binary (sonoma-arm64)	spatialDE_1.18.0.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