Changes in version 1.13.5 (2024-06-27) + add log10 as transformation method in transformAssay + add "none" as imputation method in imputeAssay + update shiny application with log10 + update vignette with log10 + update unit tests with log10 and "none" Changes in version 1.13.4 (2024-06-24) + update vignette, add information on ComBat Changes in version 1.13.3 (2024-06-21) + add functionality to perform batch correction using sva::ComBat + improve visualisation of MAplot in shinyQC Changes in version 1.13.2 (2024-06-11) + use DT::renderDT instead of shiny::renderDataTable + use DT::DTOutput instead of shiny::dataTableOutput Changes in version 1.13.1 (2024-04-25) + add batch2 and ... arguments in batchCorrectionAssay Changes in version 1.11.7 (2024-04-25) + add dplyr:: in front of pull function in vignette to avoid errors Changes in version 1.11.6 (2024-04-23) + add parameter ... to function updateSE that will be passed to SummarizedExperiment::assay within updateSE Changes in version 1.11.5 (2024-04-12) + set parameter multiplyByNormalizationValue in normalizeAssay To TRUE in shinyQC Changes in version 1.11.4 (2024-04-02) + add option to display size in dimensionReductionPlot Changes in version 1.11.3 (2024-03-20) + allow quantile normalisation (method = "quantile") for assays with columns that contain only NA values Changes in version 1.11.2 (2024-03-18) + fix warning in normalizeAssay Changes in version 1.11.1 (2024-03-15) + add parameter multiplyByNormalizationValue in normalizeAssay Changes in version 1.9.1 (2023-07-19) + fix bug in scree plot (subset the dimensionReduction object) Changes in version 1.7.7 (2023-04-20) + add package statmod to Suggests Changes in version 1.7.6 (2023-04-19) + add package jpeg to Suggests Changes in version 1.7.5 (2023-04-18) + adjust test ERROR messages Changes in version 1.7.4 (2023-01-26) + add ExperimentHub and GEOquery to NAMESPACE Changes in version 1.7.3 (2023-01-23) + use TCGA RNA-seq and cell line proteomics datasets from ExperimentHub in vignette to showcase the functionality of the package Changes in version 1.7.2 (2022-11-24) + replace aes_string by aes since aes_string is deprecated in newest ggplot2 version Changes in version 1.7.1 (2022-11-08) + adjust errors in unit tests after updating the packages Changes in version 1.5.9 (2022-10-19) + add ShinyApps to biocViews Changes in version 1.5.8 (2022-09-30) + replace vegan::metaMDS by MASS::isoMDS for NMDS dimension reduction Changes in version 1.5.7 (2022-09-29) + change renderUI functions to update...Input whenever possible + remove the dual interface for measured/missing values help pages in the values tab + improve the formula/expression checks in the DE tab using the model.matrix and makeContrasts functions Changes in version 1.5.6 (2022-09-23) + speed up non-server functions Changes in version 1.5.5 (2022-08-23) + add unit tests for imputation of missing values + bug fix (ncol instead of nrow) for calculation of BPCA imputation Changes in version 1.5.4 (2022-08-18) + improve the imputation of missing values Changes in version 1.5.3 (2022-08-01) + only use a subset of maximum 5000 features in the calculation of Hoeffding's D values. In case there are less than 10000 features in the SummarizedExperiment object, all features of the SummarizedExperiment are taken + createBoxplot precalculates the values of the boxplot instead on relying on geom_boxplot for calculation of the statistics Changes in version 1.5.2 (2022-07-20) + remove the functions biocrates, maxQuant, and spectronaut from MatrixQCvis and move to the MatrixQCUtils package Changes in version 1.5.1 (2022-07-18) + load package MatrixQCvis in report_qc.Rmd Changes in version 1.3.8 (2022-04-12) + change unit tests after changing namespace in 1.3.7 Changes in version 1.3.7 (2022-04-12) + change namespace in module_measuredValues_missingValues.R Changes in version 1.3.6 (2022-04-08) + set internally parameters (probs, batchColumn) in normalizeAssay and batchCorrectionAssay to default values when the parameters are NULL Changes in version 1.3.5 (2022-04-04) + fix error message in cvFeaturePlot after updating packages Changes in version 1.3.4 (2022-02-10) + fix bug in hoeffDValues for pivot_wider after updating tidyr (version 1.2.0) Changes in version 1.3.3 (2022-01-25) + harmonize clustering method in distShiny for columns/rows Changes in version 1.3.2 (2021-12-09) + add import of txt and xlsx files for function maxQuant + change rounding in mosaic that the plot shows more detailed numbers Changes in version 1.3.1 (2021-12-01) + use make.names for character vectors and colnames(colData(se)) in the functions for dimension reduction plot, drift plot, ECDF plot, mosaic plot, features along variable histogram, UpSet plot + add method "log" in function transformationAssay + add function spectronaut to upload spectronaut files Changes in version 1.1.3 (2021-09-30) + shift batch correction in between of normalization and transformation + add column "x5at1t1g161asy" instead of "rowname" (default) for rownames_to_column + remove the stop button and return the modified SummarizedExperiment object when stopping the shiny application, the SummarizedExperiment will be returned only when the function call is assigned to an object Changes in version 1.1.2 (2021-09-06) + take sample IDs for shinyQC from colnames(se) + take feature IDs for shinyQC from rownames(se) + fix error in report.Rmd (change input for create_boxplot to se) Changes in version 1.1.1 (2021-08-27) + fix bug in biocrates and maxQuant function Changes in version 0.99.12 (2021-05-18) + replace xlsx by openxlsx Changes in version 0.99.11 (2021-05-10) + rename function normalize to normalizeAssay + rename function transform to transformAssay + rename function batch to batchCorrectionAssay + rename function impute to imputeAssay Changes in version 0.99.10 (2021-05-06) + bump version to trigger building Changes in version 0.99.9 (2021-04-29) + add hexbin in Suggests + fix bug in MAplot that plot is displayed properly Changes in version 0.99.8 (2021-04-28) + set required version for S4Vectors to >= 0.29.15 Changes in version 0.99.7 (2021-04-28) + add version number of dependencies in Description file Changes in version 0.99.6 (2021-04-27) + add MatrixQCvis to Watched Tags on the Bioconductor support site Changes in version 0.99.5 (2021-04-27) + reduce file size of vignette by using partial_bundle for driftPlot Changes in version 0.99.4 (2021-04-26) + reduce package dependencies - remove magick - use stats::cmdscale instead of ape::pcoa - remove MsCoreUtils - remove preprocessCore - remove Matrix + add explained variance for PCoA + add se argument in create_boxplot that allows for ordering the samples + use ggplotly for driftPlot + allow flexible addition of samples in MA-plot based on a supplied character vector of sample names + return SummarizedExperiment when exiting the shiny application + add function maxQuant that allows for creation of SummarizedExperiment objects from maxQuant output (.xlsx files) Changes in version 0.99.3 (2021-03-18) + reduce file size of vignette by using partial_bundle for plotly figures Changes in version 0.99.2 (2021-03-18) + reduce resolution of images in vignette to reduce file size Changes in version 0.99.1 (2021-03-17) + reduce file size of vignette Changes in version 0.99.0 (2021-03-12) + shinyQC including visualizations/functionality for - histogram of sample types, - information on number of missing/measured values - information on (intersecting, disjoint) sets for missing/measured values - barplot and violin plot for (count/intensity) values - visualization to detect drifts/trends in (count/intensity) values - coefficients of variation for samples, - mean-sd plots, - MA plots, - empirical cumulative distribution function, - visualizations of distances between samples, - intensities of features and coefficients of variation of features, - dimension reduction plots (PCA, PCoA, NMDS, tSNE, UMAP) - differential expression + write functions for data manipulation and plots + write tests for these functions + create UI and server modules for shinyQC + write tests for UI and server modules + load different UI elements depending on the type of data (if the data contains missing values or is complete) + load different UI if the SummarizedExperiment is loaded on start of shinyQC or not