Plugins are apps that extend functionality of FlowJo™, which may be developed by 3rd-party developers or by the team at FlowJo, LLC.
To learn more, please see Installing a Plugin and to learn about the available plugins:
tSNE: reduce your data to 2 dimensions
Downsample: create a new gate which selects a limited number of data points/events from a sample or gated population
SPADE: visualize high-dimensional flow and mass cytometry data
CellOntology: determine the name or etiology of a gated cell/ population in question