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