https://github.com/sales-lab/spatialde
R wrapper for SpatialDE
https://github.com/sales-lab/spatialde
python r spatial-data transcriptomics wrapper
Last synced: 9 months ago
JSON representation
R wrapper for SpatialDE
- Host: GitHub
- URL: https://github.com/sales-lab/spatialde
- Owner: sales-lab
- License: other
- Created: 2020-12-18T11:18:55.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2025-04-16T06:27:37.000Z (10 months ago)
- Last Synced: 2025-05-05T03:17:57.608Z (9 months ago)
- Topics: python, r, spatial-data, transcriptomics, wrapper
- Language: R
- Homepage:
- Size: 1.47 MB
- Stars: 3
- Watchers: 3
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# spatialDE
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/sales-lab/spatialDE/actions)
[](https://codecov.io/gh/sales-lab/spatialDE?branch=main)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/spatialDE)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/spatialDE)
The **spatialDE** package provides an R wrapper for the Python SpatialDE library,
using `r BiocStyle::CRANpkg("reticulate")` and `r BiocStyle::Biocpkg("basilisk")`.
[SpatialDE](https://github.com/Teichlab/SpatialDE), by [Svensson et al., 2018][Svensson2018],
is a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.
This package started as part of the
[BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then
install `r BiocStyle::Biocpkg("spatialDE")` from
[*Bioconductor*](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("spatialDE")
```
The development version of **spatialDE** can be installed from
[GitHub](https://github.com/sales-lab/spatialDE) with:
```{r 'install_dev', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
BiocManager::install("sales-lab/spatialDE")
```
## Basic usage
```{r usage, eval=TRUE}
library(spatialDE)
spe <- mockSVG(return_SPE = TRUE)
de_results <- spatialDE(spe)
head(de_results)
```
## Citation
Below is the citation output from using `citation('spatialDE')` in R. Please
run this yourself to check for any updates on how to cite __spatialDE__.
Please note that this package merely provides a wrapper to use the original Python methods in R. If you find these methods useful, please also consider citing the [original paper][Svensson2018].
```{r 'citation', eval = requireNamespace('spatialDE'), echo = FALSE, comment = ""}
print(citation('spatialDE'), bibtex = TRUE)
```
## Code of Conduct
Please note that the **spatialDE** project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
## Useful links
- `r BiocStyle::Biocpkg("SpatialExperiment")`
- [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
[Svensson2018]: https://doi.org/10.1038/nmeth.4636