spatialDE
R wrapper for SpatialDE
Bioconductor version: Release (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 (from within R, enter
citation("spatialDE")):
Installation
To install this package, start R (version "4.4") 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 | ||
| LICENSE | Text |
Details
| biocViews | Software, Transcriptomics |
| Version | 1.12.0 |
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | spatialDE_1.12.0.zip |
| macOS Binary (x86_64) | spatialDE_1.12.0.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 |