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In recent years flow cytometry instrumentation has evolved rapidly, allowing researchers to interrogate an increasingly higher number of phenotypic and functional markers in a single experiment. However, increasing the number of measured parameters also increases the complexity of data analysis, as there are simply too many possible combinations of markers to define and compare using standard hierarchical gating. As a result, dimensionality reduction (DR) and clustering algorithms are being employed frequently as an alternative to standard gating for known populations. However, the caveat to DR is that for multiple samples or experimental conditions to be compared in a dimensionally reduced data space, the DR step must be performed on all data merged together, not separately on individual samples. Join us for an introduction to the discovery workflow of concatenation → tSNE → clustering, which allows for identification of previously unknown populations that are changing between different experimental conditions.