Changes in Version 2.1.2 (2021-05-13)

 * Added diffAbundanceFET and plotClusterAbundance function
 * Linked Shiny UI help buttons to new online help pages

 * Expanded convertSCEtoSeurat() function to copy additional data

 * Updated and merged pkgdown documentation
 * Added HTML reports for Seurat curated workflow and marker finding

 * Refactor of Normalization UI
 * Added tagging system for matrix type
 * Several bug fixes

 * Added generic wrapper functions for normalization, dimensionality reduction and feature selection

 
 Changes in Version 2.0.1 (2021-01-07)
 
 * Added cell type labeling functional, wrapping SingleR method
 * Added cell type labeling UI under differential expression tab
 * Added marker identification in Seurat workflow
 

 Changes in Version 2.0.0 (2020-10-16)
 
 * Added quality control (empty droplet detection, doublet detection, etc) functionality
 * Ability to import data from varying preprocessing tools
 * Ability to export SingleCellExperiment object as varying file types (flat file, Python anndata)
 * Added functions for visualization of data
 * New CellViewer functionality in UI
 * Improvements to differential expression, now includes DESeq2, limma, ANOVA
 * Incorporates Seurat workflow
 

 Changes in Version 1.1.26 (2018-10-23)
 
 * New UI design for the Differential Expression tab.
 * New UI design for the Data Summary & Filtering tab.
 * Support for additional assay modification including log transforming any assay and renaming assays.
 * New function visPlot for creating scatterplots, boxplots, heatmaps, and barplots for custom gene sets.
 * The Downsample tab now works on a generic counts matrix
 * You can upload a SCtkExperiment object or a SingleCellExperiment object saved in an RDS file on the Upload tab.
 * Differential Expression results can now be saved in the rowData of the object and loaded for later analysis.
 * Improved ability to save a biomarker based on user options.
 * The Differential Expression plot is not automatically created, for more user control with large datasets.
 

 Changes in Version 1.1.3
 

 * Improvements to plotting, change text size and hide labels in gsva plots.
 * MAST violin and linear model plots are now more square when plotting less than 49 facets.

 * Changed y axis label in plotBatchVariance to "Percent Explained Variation"
 

 Changes in Version 1.1.2
 
 * Ability to hide version number in the SCTK GUI.
 
 Changes in Version 1.1.1
 
 * Fixed a bug that would cause the diffex color bar to not display when special
 characters were in the annotation.
 

 Changes in Version 0.99.3
 
 * Consistent use of camel case throughout package
 

 Changes in Version 0.6.3
 
 * Additional links to help documentation
 * Example matrices on upload page.
 

 Changes in Version 0.4.7
 
 * Ability to download/reupload annotation data frame and convert annotations to
 factors/numerics
 

 Changes in Version 0.4.5
 
 * Documentation updates to fix NOTES and pass BiocCheck