Changes in version 1.17.1 (2025-06-26)
+ fix error with respect to setExperimentHubOption in vignette

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