reComBat-seq: Regularized negative binomial regression for batch-effect correction in underdetermined transcriptomics datasets (opens in new tab)

Motivation: Batch effect correction is essential for the integration of large-scale transcriptomics datasets such as single-cell RNA-seq or multi-study bulk RNA-seq datasets for reducing technical noise that may mask biological signal. Existing correction methods, either do not produce count data output which is crucial for state-of-the-art downstream analyses such as differential expression analysis or fail to converge in underdetermined study designs. Results: We present reComBat-seq, a met...