BEER

BEER (Batch EffEct Remover) is an R tool to detect and remove batch effects in single-cell RNA-seq data. The BEER algorithm converts data into one-dimensional values by stochastically embedding neighboring tSNEs and groups the cells and evaluates the expression profiles. It uses Kendall’s tau to determine cell-pair distances. It detects and removes batch effects using the fastMNN method, which identifies mutual nearest neighbor cells in separate batches. The BEER also has a workflow for users to learn the potential biological significance of removed PCs.