spatialDE
This is the development version of spatialDE; for the stable release version, see spatialDE.
R wrapper for SpatialDE
Bioconductor version: Development (3.20)
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] , Milan Malfait [aut]
, Lambda Moses [aut]
, Gabriele Sales [cre]
Maintainer: Gabriele Sales <gabriele.sales at unipd.it>
citation("spatialDE")
):
Installation
To install this package, start R (version "4.4") 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 | ||
LICENSE | Text |
Details
biocViews | Software, Transcriptomics |
Version | 1.11.0 |
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 |
See More
Suggests | knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | spatialDE_1.11.0.tar.gz |
Windows Binary | spatialDE_1.11.0.zip |
macOS Binary (x86_64) | spatialDE_1.11.0.tgz |
macOS Binary (arm64) | spatialDE_1.11.0.tgz |
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 |