Changes in version 2.14.0 (2024-05-03) - Updated version to match Bioconductor 3.19 - Update runGSVA fucntion 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