Fig. 1

The MBECS processing pipeline comprises five main steps that provide users with the means to investigate potential batch effects and mitigate them before downstream statistical analyses: The preliminary report provides an overview of a data set to assess the presence and gravity of batch effects. The correction step can apply and store the output of various BECAs. The available correction methods are Remove Unwanted Variation 3 (ruv3), Batch Mean Centering (bmc), ComBat (bat), RemoveBatchEffects (rbe), Percentile Normalization (pn), and Singular Value Decomposition (svd). Several variance assessment methods, e.g., linear modeling, principal variance component analysis, and redundancy analysis are employed in the post-processing reports to produce a comparative qualitative analysis between the uncorrected data set and the selected BECAs. The export functionality allows extraction of the transformed or corrected counts in tabular or phyloseq formats to facilitate downstream statistical analyses