spatialDE

R wrapper for SpatialDE

Bioconductor version: 3.24 · Package version: 1.19.0

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.

Installation

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

BiocManager::install("spatialDE")

Details

Maintainer	Gabriele Sales <gabriele.sales@unipd.it>
Author	Davide Corso [aut] (ORCID: <https://orcid.org/0000-0001-8845-3693>), Milan Malfait [aut] (ORCID: <https://orcid.org/0000-0001-9144-3701>), Lambda Moses [aut] (ORCID: <https://orcid.org/0000-0002-7092-9427>), Gabriele Sales [cre]
License	MIT + file LICENSE
URL	https://github.com/sales-lab/spatialDE, https://bioconductor.org/packages/spatialDE/
Bug Reports	https://github.com/sales-lab/spatialDE/issues
Downloads rank	475
Source branch	devel
biocViews	Software, Transcriptomics

Documentation

Introduction to spatialDE

Download

Follow the installation instructions to use this package in your R session.

Source package	spatialDE_1.19.0.tar.gz
Windows binary (x86_64)	spatialDE_1.19.0.zip
macOS binary (arm64)	spatialDE_1.19.0.tgz
macOS binary (x86_64)	spatialDE_1.19.0.tgz

Dependencies

Depends: R (>= 4.3)

Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra

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