• Major improvements & bug fixes from SeqGeq v1.0.1
  • 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
  • New and improved demo data file for Melanoma data matrix from Tirosh, et al.


  • tSNE run on subpopulations
  • tSNE run on raw expression matrix (not recommended), as opposed to principal components, will now produce a sensible plot
  • Dot plot overlays now supported
  • Synthetic parameter histograms correctly graphed
  • Analyses no longer lose their associated raw data

Known Issues

  • “Export Eigen Vectors” button from Principal Component type Dimensionality Reduction dialog is not functioning.
  • Only demo data can be loaded when running SeqGeq in demo mode; i.e. concatenated data (even from demo files) cannot be loaded into SeqGeq in demo mode.
  • Some hotkeys meant to open tabs in the Workspace will generate a bug report window.
  • Bug reporting window does not send information to FlowJo, LLC. Workaround: Send an email to tech support for a speedy reply and troubleshooting: seqgeq@flowjo.com
  • The 24 hour authentication grace period for temporary offline access will sometimes fail to correctly activate.
  • 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.
  • For long x-axis names, the color mapping key can overlap this annotation. Workaround: Reduce the size of the x-axis annotation from the Graph Definition window.
  • 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.
  • DRP wait time warning messages are overly conservative and need recalibration.

If you have any questions or comments regarding the SeqGeq platform we greatly appreciate any feedback.