Changelog

Source: NEWS.md

Changes in Version 2.16.1 (2024-02-12)

• Fixed decontX/soupX webapp error
• Fixed error in reportCellQC
• Fixed additional bugs with Seurat V5 integration

Changes in Version 2.16.0 (2024-10-29)

• Updated version to match Bioconductor 3.20

Changes in Version 2.14.0 (2024-05-03)

• Updated version to match Bioconductor 3.19
• Update runGSVA function to work with newer GSVA package

Changes in Version 2.12.2 (2024-01-28)

• Added support for Seurat V5

Changes in Version 2.12.1 (2024-01-10)

• Updates to documentation
• Fixes to runTSCAN and plotSeurat Genes
• Added support for flat file import into SCTK-QC
• Fixed directory issue in importCellRanger
• Added Bubble plot to Shiny GUI
• Updated Dockerfile

Changes in Version 2.12.0 (2023-10-24)

• Updated version to match Bioconductor 3.18

Changes in Version 2.10.1 (2023-07-26)

• Added function for bubble plot
• In SCTK-QC pipeline, added support for batch processing multiple inputs
• In SCTK-QC pipeline, added support for importing and exporting AnnData objects
• In SCTK-QC pipeline, fixed a bug causing YAML output files to be empty
• Update the SCTK-QC tutorial
• Fixed bug in combineSCE causing it to create multiple copies of row or column data

Changes in Version 2.10.0 (2023-04-25)

• Updated version to match Bioconductor 3.17

Changes in Version 2.8.1 (2023-03-10)

• Added scanpy wrapper functions for use from console
• Added scanpy UI curated workflow
• Integrated scanpy to a la carte workflow
• Fixed a bug in importing fluidigm dataset
• Updated downloading features in the Shiny app
• Added error checking around Enrichr functions
• Minor tweaks to plot defaults

Changes in Version 2.8.0 (2022-12-19)

• Updated version to match Bioconductor version

Changes in Version 2.7.3 (2022-10-25)

• Fixed bugs related to dependency updates

Changes in Version 2.7.2 (2022-10-19)

• Deprecated findMarkerDiffExp(), findMarkerTopTable() and plotMarkerDiffExp(), which are replaced by runFindMarker(), getFindMarkerTopTable() and plotFindMarkerHeatmap(), respectively
• Added useReducedDim, detectThresh arguments for find marker functions
• Deprecated getUMAP() and getTSNE(), which are replaced by runUMAP() and runTSNE(), respectively
• Added runQuickUMAP() and runQuickTSNE() functions which directly compute the proper embedding from raw counts matrices with a simplified argument set
• Added arguments aggregateRow and aggregateCol to plotSCEHeatmap()
• Updated output metadata structure of QC functions, as well as combineSCE() which merges the new structure properly
• Refined batch correction function set
• Fixed bugs related to UI and console functions

Changes in Version 2.7.1 (2022-06-29)

• 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

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