BatChef

BatChef is an R package that:

• implements a variety of correction methods;

• provides quantitative metrics to evaluate the performance of the correction methods, including the Wasserstein distance, Local Inverse Simpson's Index (LISI), Average Silhouette Width (ASW), and Adjusted Rand Index (ARI);

• can be used as a guideline to identify the most appropriate batch effects correction method based on data-specific characteristics.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("BatChef")