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)).

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.

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

BiocManager::install("christinehou11/BatchSVG")

Code of Conduct

Please note that the BatchSVG project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.