BatchSVG

BatchSVG is a feature-based Quality Control (QC) to identify SVGs on spatial transcriptomics data with specific types of batch effect. Regarding to the spatial transcriptomics data experients, the batch can be defined as “sample”, “sex”, and etc.The BatchSVG method is based on binomial deviance model (Townes et al, 2019)) and applies cutoffs based on the number of standard deviation (nSD) of relative change in deviance and rank difference as the data-driven thresholding approach to detect the batch-biased outliers.

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.