• Introducing the Geneset Enrichment platform, accessible by right clicking on a gene set.
  • Multigraph Color Mapping  feature in “Multigraph Overlay” section of Layout Editor plot right click drop down menu.
  • New multi-omics demo data set for Systemic Lupus Erythematosus (SLE) provided by Accelerating Medicines Partnership consortium.
  • Proxy credentials dialog now available when no internet connection is detected.


  • Export collections in GMT format for use as library in Geneset Enrichment.
  • False Discovery Rate (FDR) p-value correction now available as well as the default Bonferroni.


  • Resolved issue illustrating scale of Fold Change for certain population comparisons in SeqGeq v1.2.
  • Transform settings now saved for populations in Gene View.

Known Issues

  • Legacy workspaces with gates drawn in Gene View will need to be re-confirmed, as changes in this version may have altered their position or geometry.
  • “Export Eigen Vectors” button from Principal Component type Dimensionality Reduction dialog for Windows will default to save the vectors in a temporary forlder. Workaround: Make sure to save vectors to a common location, such as Desktop.
  • Changes to Gene View dot sizes are not saved. Workaround: Adjust dot sizes in the Display tab of the Graph Window.
  • Bring forward command in Layout Editor gives bug reporting window. Workaround: Close the bug report window and continue analysis.
  • Derived Observations (e.g. PCA vectors) calculated for certain Derived Parameters (e.g. a Gene Set in Cell View) will not be correctly applied when re-opening a saved analyses. Workaround: Don’t apply Derived Observations to Derived Parameters.
  • 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.
  • 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.