A normalization tool for the removal of batch effects in cytometry data. CytoNorm makes use of control samples taken along in every batch to learn the technical differences between the batches. Cell-type specific batch effects can be captured thanks to a FlowSOM clustering step, and non-linear changes are modeled by characterizing the distributions with multiple quantiles and aligning them with splines. Available on Github, Bioconductor and FlowJo.