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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
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# spatialDE
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<!-- badges: start -->
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[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/sales-lab/spatialDE/actions)
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[](https://codecov.io/gh/sales-lab/spatialDE?branch=main)
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[](https://bioconductor.org/checkResults/release/bioc-LATEST/spatialDE)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/spatialDE)
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<!-- badges: end -->
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The **spatialDE** package provides an R wrapper for the Python SpatialDE library,
using `r BiocStyle::CRANpkg("reticulate")` and `r BiocStyle::Biocpkg("basilisk")`.
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[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
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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:
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```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
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BiocManager::install("spatialDE")
```
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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")
```
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## Basic usage
```{r usage, eval=TRUE}
library(spatialDE)
spe <- mockSVG(return_SPE = TRUE)
de_results <- spatialDE(spe)
head(de_results)
```
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## 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.
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## Useful links
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- `r BiocStyle::Biocpkg("SpatialExperiment")`
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- [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)
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This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
[Svensson2018]: https://doi.org/10.1038/nmeth.4636
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