• 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.

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.

Requests to improve plot resolution have been heard! SeqGeq now has options to customize the resolution of plots, change the shape of dots in plots, and adjust their sizes as well—even on a layer by layer basis in dot plot overlays. This uncovers some really beautiful new possibilities for figure generation.

• Mouse-Over Information shown for both cells and genes within Graph Windows. This means that researchers can now very quickly determine the identity of individual dots in their plots with ease. We’ve also added the ability to “pin” the parameter names in GeneView plots to graphs within the Layout Editor, so that these annotations become available for export and publication. 
• High-Resolution Figures—up to 4096 x 4096 pixels—are now available. This will make your figures for publication pop in a way never before possible. In addition, the seed for contour plots is now adjustable in order to better illustrate populations of any size within that plot type. 
• Dot Shapes can be adjusted within dot plots and dot plot overlays in the Layout Editor. Dot Sizes are also now editable on a layer by layer basis within the overlays. 

These are just a few of the many improvements available in SeqGeq v1.6

• Introducing a Normalization Platform – Now available in the Discovery band of the Workspace, which allows researchers to run normalization across parameter-sets in data matrices.
• Multi-Geneset Enrichment Analysis - Simply select multiple genesets and run the enrichment platform against a geneset library (GMT) of your choice.
• Opt-SNE algorithm enabled! This means researchers won’t usually need to try and find optimal tSNE settings for their data if they use the default settings (Opt-SNE enabled). The algorithm uses KLD to find appropriate cut-offs in iterations.
• Derived Observations of Genes used to identify genes in analytical genesets (gating in geneview) will now be included in Geneset inspector, and exports. This means that researchers can now export q-Value statistics, Fold-Changes, and more.

Highlights

• Introducing a Clustering Platform - Now available in the Discovery band of the Workspace, which allows researchers to run KMeans clustering and KNearest-Neighbors (KNN) classification.

• Genes illustrated in the Pivot Window (i.e. Gene View) can now be selected and filtered in the top left hand corner of the Graph Window. This allows researchers to focus only on parameters of interest when gating in Gene View.

Improvements

• PCA now contains options to normalize and log transform parameters used for the dimensionality reduction, greatly improving the resulting clustering.

• Optimizations to the tSNE algorithm to increase efficiency of the calculation.

• Support for sparse expression matrix ".st" file types.

• Support for synthetic parameters, such as GeneSets, in multigraph color maps.

• Release notification mechanism to let users know when the next release becomes available. (Active for releases post SeqGeq v1.4.0)

Fixes

• Adjustments to p-value calculations in volcano plots.

• Axes labels for Gene View plots in the Layout Editor can now be edited from the Graph Definition window.

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

Highlights

• 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.

• 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.
• Full Release Notes

• Significant speed Improvements in the Dimensionality Reduction Platform

• Many issues found in SeqGeq 1.0 have been fixed

• Full Release Notes

• 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

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.

Requests to improve plot resolution have been heard! SeqGeq now has options to customize the resolution of plots, change the shape of dots in plots, and adjust their sizes as well—even on a layer by layer basis in dot plot overlays. This uncovers some really beautiful new possibilities for figure generation.

• Mouse-Over Information shown for both cells and genes within Graph Windows. This means that researchers can now very quickly determine the identity of individual dots in their plots with ease. We’ve also added the ability to “pin” the parameter names in GeneView plots to graphs within the Layout Editor, so that these annotations become available for export and publication. 
• High-Resolution Figures—up to 4096 x 4096 pixels—are now available. This will make your figures for publication pop in a way never before possible. In addition, the seed for contour plots is now adjustable in order to better illustrate populations of any size within that plot type. 
• Dot Shapes can be adjusted within dot plots and dot plot overlays in the Layout Editor. Dot Sizes are also now editable on a layer by layer basis within the overlays. 

These are just a few of the many improvements available in SeqGeq v1.6

• Introducing a Normalization Platform – Now available in the Discovery band of the Workspace, which allows researchers to run normalization across parameter-sets in data matrices.
• Multi-Geneset Enrichment Analysis - Simply select multiple genesets and run the enrichment platform against a geneset library (GMT) of your choice.
• Opt-SNE algorithm enabled! This means researchers won’t usually need to try and find optimal tSNE settings for their data if they use the default settings (Opt-SNE enabled). The algorithm uses KLD to find appropriate cut-offs in iterations.
• Derived Observations of Genes used to identify genes in analytical genesets (gating in geneview) will now be included in Geneset inspector, and exports. This means that researchers can now export q-Value statistics, Fold-Changes, and more.

Highlights

• Introducing a Clustering Platform - Now available in the Discovery band of the Workspace, which allows researchers to run KMeans clustering and KNearest-Neighbors (KNN) classification.

• Genes illustrated in the Pivot Window (i.e. Gene View) can now be selected and filtered in the top left hand corner of the Graph Window. This allows researchers to focus only on parameters of interest when gating in Gene View.

Improvements

• PCA now contains options to normalize and log transform parameters used for the dimensionality reduction, greatly improving the resulting clustering.

• Optimizations to the tSNE algorithm to increase efficiency of the calculation.

• Support for sparse expression matrix ".st" file types.

• Support for synthetic parameters, such as GeneSets, in multigraph color maps.

• Release notification mechanism to let users know when the next release becomes available. (Active for releases post SeqGeq v1.4.0)

Fixes

• Adjustments to p-value calculations in volcano plots.

• Axes labels for Gene View plots in the Layout Editor can now be edited from the Graph Definition window.

Highlights

• 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.

• 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.
• Full Release Notes

• Significant speed Improvements in the Dimensionality Reduction Platform

• Many issues found in SeqGeq 1.0 have been fixed

• Full Release Notes