• This release is NOT certified by FlowJo, LLC Quality Assurance Department.
  • This release is not for production use.
  • Major improvements & bug fixes from SeqGeq v1.0.1, including Plugin API feature. Initial plugins are available on The FlowJo Exchange.


  • Enhanced performance
  • Support for HDF5 (.h5) formatted data files
  • Color mapping key for plots in layouts
  • Support for Plugins


  • tSNE run on subpopulations
  • Dot plot overlays
  • Synthetic parameter histograms
  • And many others

Known Issues

  • Some hotkeys meant to open tabs in the Workspace will generate a bug report window.
  • DRP wait time warning messages are overly conservative and need recalibration.
  • On a Mac, R-based plugins fail to calculate if the file paths contains a space or other special characters. Workaround: Remove spaces and special characters from file paths associated with the analysis.
  • Running tSNE on a raw expression matrix is not advised. Workaround: We recommend running tSNE on principal components, after running PCA on the expression matrix of interest.
  • Using “Deviation from Median” normalization on gene sets in the graph window can cause a crash on Windows. Workaround: Use another normalization, such as Geometric Mean or Median.

If you choose to test this software we greatly appreciate any feedback.