singleCellTK release v2.7.1

• Refactored scaling related parts of the workflow, including variable feature detection, dimension reduction and 2D embedding
• Redesigned UI landing page and UI running prompt
• Added marker table module across UI
• Added more unit tests
• Fixed bugs in TSCAN UI
• Other minor bug fixes

singleCellTK release v2.6.0

• 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

singleCellTK release v2.5.1

• 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

singleCellTK release v2.4.1

• Added new function fora 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

singleCellTK release v2.4.0

Changes in Version 2.4.0 (2021-10-27)

• Updated version to match Bioconductor

Changes in Version 2.3.2 (2021-10-24)

• Added summary table into the cellQC report
• Improved formatting in QC report
• Added functions getDEGTopTable() & plotBatchCorrCompare()
• Other refactors and bug fixes

singleCellTK release v2.2.2

• 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

v2.0.2

• 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

v2.0.1

• Added cell type labeling functional, wrapping SingleR method
• Added cell type labeling UI under differential expression tab
• Added marker identification in Seurat workflow