- Updated version to match Bioconductor
- Added Seurat report functions
- Added TSCAN trajectory analysis functions
- Refactored EnrichR wrapper function (runEnrichR)
- Added new cut-offs for DE functions
- Other refactors and bug fixes
- Added SoupX method for decontamination (runSoupX)
- Added useReducedDim parameter for DE analysis and Heatmap
- Added Differential Abundance section to the tutorials
- Fixed Mitochondrial gene list
- Other refactors and bug fixes
- Added new function for DEG volcano plot (plotDEGVolcano)
- Added new function for plotting pathway scores (plotPathway)
- Added Pathway Analysis section to the tutorials
- Added seed parameter to several functions and UI for reproducibility
- Updated R console and GUI tutorials to match each other
- Fixed console logging in the GUI
- Updated version to match Bioconductor
- Added summary table into the cellQC report
- Improved formatting in QC report
- Added functions getDEGTopTable() & plotBatchCorrCompare()
- Other refactors and bug fixes
- Several bug fixes
- 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
- Added diffAbundanceFET and plotClusterAbundance function
- Linked Shiny UI help buttons to new online help pages
- Several bug fixes
- 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
- Added cell type labeling functional, wrapping SingleR method
- Added cell type labeling UI under differential expression tab
- Added marker identification in Seurat workflow
- 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
- 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.
- 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"
- Ability to hide version number in the SCTK GUI.
- Fixed a bug that would cause the diffex color bar to not display when special characters were in the annotation.
- Consistent use of camel case throughout package
- Additional links to help documentation
- Example matrices on upload page.
- Ability to download/reupload annotation data frame and convert annotations to factors/numerics
- Documentation updates to fix NOTES and pass BiocCheck