Recent developments in technology have enabled the exploration of complex biological systems at the single cell level, leading to new insights in the way the immune system is regulated in conditions such as cancer or auto-immune disorders. One of these technologies, mass cytometry, is now being applied in the context of clinical trials as a way to gain insights into the mechanism of action of treatments, as well as to unravel determinants of patient response. These new applications pose significant challenges for data analysis, and in this presentation Yann Abraham, a computational immunologist with Janssen Pharmaceutical, will cover issues such as quality control, batch correction and single cell differential analysis, and the computational solutions that have been developed to address them.