Changes in Version 2.2.2 (2021-10-10)

* Several enhancements, refactors, and bug fixes to the UI
* Refactor documentation and pkgdown site
* Added tutorials for R console analysis
* Updates to the UMAP generation in the SCTK-QC pipeline
* Addition of VAM to Pathway prediction tab
* Bug fix to the mitochondrial gene set functions

Changes in Version 2.1.3 (2021-05-14)

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

Changes in Version 2.0.2 (2021-05-08)

* Expanded convertSCEtoSeurat() function to copy additional data
* Updated and merged pkgdown docs
* Added HTML reports for Seurat curated workflow
* Refactor of Normalization UI
* Added generic wrapper function for dimensionality reduction
* Added tagging system for matrix type
* Several bug fixes
* Added missing documentation
* Added wrapper functions for normalization, dimensionality reduction and feature selection
* Added function seuratReport() to generate a seurat report from input SCE object

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
