Highlights:
- SeqGeq has been rebuilt to run on Java 8 to increase security as Java 9 has not been updated since 2018.
SeqGeq build includes the Zulu JRE 8u312b07 with OpenJFX. The Windows release is listed as 8.58.0.13 (released in October 2021), and the macOS release is listed as 8.58.0.53 (released in November 2021). - Speed improvements with the newer build.
Known Issues:
- Dark Mode on Mac BigSur and newer induce reading difficulties due to contrast issue on some buttons/functionalities. Workaround: Change your OS appearance to “Light Mode”: System Preferences > General > Appearance: Light.
- 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.