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Bioconductor - spatialDE (development version)

spatialDE

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

R wrapper for SpatialDE

Bioconductor version: Development (3.22)

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")): 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")
Details biocViews Software, Transcriptomics Version 1.15.1 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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 See More Package Archives

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

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