Changelog

Source: NEWS.md

Changes in Version 2.6.0 (2022-04-28)

  • Updated version to match Bioconductor

Changes in Version 2.5.2 (2022-04-23)

  • 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

Changes in Version 2.5.1 (2022-03-31)

  • 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

Changes in Version 2.4.1 (2021-12-22)

  • 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

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

Changes in Version 2.3.1 (2021-10-15)

  • Several bug fixes

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