To cite FlowSOM in publications use:

  Van Gassen S et al. (2015) FlowSOM: Using self-organizing maps for
  visualization and interpretation of cytometry data. Cytom Part J Int
  Soc Anal Cytol 87: 636-645.
  https://onlinelibrary.wiley.com/doi/full/10.1002/cyto.a.22625

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{FlowSOM}: Using self-organizing maps for visualization and interpretation of cytometry data},
    author = {Sofie {Van Gassen} and Britt Callebaut and Mary J {Van Helden} and Bart N Lambrecht and Piet Demeester and Tom Dhaene and Yvan Saeys},
    journal = {Cytometry Part A},
    year = {2015},
    volume = {87},
    number = {7},
    pages = {636-645},
    url = {https://onlinelibrary.wiley.com/doi/full/10.1002/cyto.a.22625},
  }