https://github.com/christinehou11/batchsvg
Identification of biased features from SVGs in spatial transcriptomics data
https://github.com/christinehou11/batchsvg
batch-effect bioconductor-package spatial-transcriptomics
Last synced: 24 days ago
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Identification of biased features from SVGs in spatial transcriptomics data
- Host: GitHub
- URL: https://github.com/christinehou11/batchsvg
- Owner: christinehou11
- Created: 2024-10-18T01:53:17.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-12-04T22:49:26.000Z (4 months ago)
- Last Synced: 2025-12-08T06:53:51.073Z (3 months ago)
- Topics: batch-effect, bioconductor-package, spatial-transcriptomics
- Language: R
- Homepage: https://christinehou11.github.io/BatchSVG/
- Size: 16.7 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
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README
## BatchSVG
`BatchSVG` is a method to identify
batch-biased spatially variable genes (SVGs) in spatial transcriptomics data.
The batch variable can be defined as "sample", "donor sex", or other batch effects of interest. The `BatchSVG` method is based on the
binomial deviance model ([Townes et al, 2019](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1861-6))).
#### Installation
`BatchSVG` is a R package available in *Bioconductor* version 3.19 and later.
You can install `BatchSVG` by using the following commands in R session from
*Bioconductor*.
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("BatchSVG")
## Check that you have a valid Bioconductor installation
BiocManager::valid()
```
The development version can be obtained by
``` r
BiocManager::install("christinehou11/BatchSVG")
```
### Code of Conduct
Please note that the BatchSVG project is released with
a [Contributor Code of Conduct](https://christinehou11.github.io/BatchSVG/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.