forked from sales-lab/spatialDE
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathREADME.Rmd
95 lines (64 loc) · 3.34 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
---
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%"
)
```
# spatialDE
<!-- badges: start -->
[](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)
<!-- badges: end -->
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