Highlights

• Issues with the “Save” function have been fixed. This extends to the auto-save dialog created when closing a workspace. It should no longer be necessary to always use the “Save As” function and make successive versions, or save excessive copies of .geqzip analysis files.
• SeqGeq has been updated to run with Java 9.
• Single cell heatmap data in Layouts is now cached so updates to heatmaps following their initial creation will be faster.

Fixes

• Parameters with (Ab) in the name no longer get another (Ab) tag added to the name.
• Some hotkeys meant to open tabs in the workspace will no longer result in a contact flowjo window.
• The Layout Editor Bring Forward command no longer results in a contact flowjo window.

Known Issues

• Certain legacy workspace Layouts cannot be loaded into the latest release. Workaround: keep the older version of SeqGeq in order to access the previous work completed there, use the new edition to analyze new datasets.
• Lex cannot de-multiplex populations combined directly from within a single sample. Workaround: Export subset populations as individual and properly named samples prior to concatenation.
• Editor. Workaround: “Fake the overlay” by aligning plots of interest horizontally an vertically, with the topmost plot’s background set to clear. Make sure to place the smaller of the two genesets on top.
• Non-Unicode 8 characters (such as those in the Chinese alphabets) in a dataset’s file path will prevent data from being loaded into SeqGeq workspaces on Windows machines. Workaround: Make sure the file path leading to Gene Expression matrices are using only standard English character sets.
• Heatmapping downsampled populations can lead to blank rows. Workaround: Downsample populations manually, as opposed to using the Downsampling platform when heatmapping downstream.
• KMeans clustering does not perform an autogate to illustrate clusters as populations in the workspace. Workaround: Run the AutoGateCategorical plugin on the KMeans clustering parameter to identify those subpopulations.
• Gating path names longer than about 30 characters cause errors in calculating p-Values in Gene View Workaround: Name populations judiciously.
• 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.
• 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.
• 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.
• Parameter Selector for plugins won’t discriminate between identical samples opened in different workspaces (and uses the first workspace only). Workaround: Don’t open the same dataset in different workspaces simultaneously while attempting to access plugins.