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