- Speed of the Dimensionality Reduction Platform has been significantly improved.
- Many issues found in SeqGeq 1.0 have been fixed.
Dimensionality Reduction Platform
- Dimensionality Reduction Platform (DRP) runs significantly faster than previously.
- PCA now operates normally when the sample contains non-numerical metadata.
- Running a dimensional reduction algorithm on genes whose names do not start with the word “metadata” no longer causes a crash.
- When running dimensionality reduction algorithms, progress bars and warnings now estimate completion times more accurately.
- When running a dimensionality reduction algorithm, the progress bar shows the correct progress of the algorithm.
- An enhanced file format inference mechanism successfully handles files without cell IDs in paramsInRows format, and malformed files that have no header in the first column.
- SeqGeq is better able to read files containing ambiguous gene labels or inconsistent row or column formats, including files with the .tab extension.
- Support for exporting SVG files on the Mac OS has been restored.
- Support for exporting PDF files on the Mac OS has been restored.
Gene Sets Panel
- The Gene Set Inspector now shows the correct Created and Modified dates.
- When re-importing an exported CSV gene set file into the original workspace, the resulting gene set retains the file’s name, and does not overwrite the original gene set in the workspace.
- If a workspace contains data files with different sets of genes, the Graph window only allows selection of genes that exist in the subpopulation being displayed.
- When plotting two parameters, then overlaying a heatmap of a third parameter, cells that have parameter values of 0 display as light gray. In version 1.0, these did not display at all.
- When switching the Y axis to a derived parameter, the events plot correctly.
- After running PCA to create analytic parameters with Performance preferences set to use the minimum cache size, flushing the cache (such as by loading another data file) no longer affects the data output in the Graph window.
- Adding a new boolean gate no longer affects gate statistics.
- When dropping populations into the bottom-rightmost chart in the Layout Editor, the chart updates correctly.
- When iterating by keyword on two cell populations in a layout, setting the Iterate By field to Keyword, then to Sample, then back to Keyword no longer causes a crash when attempting to set the Value field to a value other than 1.
- Dragging bands from the Ribbon Configuration window to the Ribbon now works normally on the Mac OS. Note that the Ribbon Configuration window must not overlap the Workspace window for dragging to work properly.
- Saving the workspace while a data file is importing no longer causes an error.
- After adding a population of cells to an opened file and then saving the file, SeqGeq saves the changes to the original file instead of creating a new file.
Dimensionality Reduction Platform
- When opening the DRP dialog box while multiple subpopulations having overlapping events are selected, the overlapping events are counted separately. As a result, the DRP dialog box shows an inflated number of total events.
- Concatenating files occasionally causes crashes.
- Workaround: Save the workspace before concatenating.
- When exporting/concatenating CSV samples with All Genes selected and with both New Workspace and Existing Workspace unchecked, SeqGeq crashes after the file placement prompt appears.
- Workaround: Save the workspace before concatenating or exporting.
- When several Graph Windows are open, an open Graph Window can change from another type of plot to a contour plot.
- Workaround: Change the plot back to its original type.
- After deleting a graph in the Layout Editor, Undo does not bring the graph back.
- When creating a heatmapped layout, SeqGeq does not warn you if the number of rows in the layout is too large for your computer’s memory to calculate, potentially causing the application to run out of memory and freeze.
- Workaround: Save the workspace before creating large heatmaps.
- On the Mac OS, if the Workspace window is dragged underneath the Ribbon Configuration window, bands cannot be dragged to the Ribbon.