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