Changes in version 0.99.10                       

  - Dependency packages:
      - we remove unnecessary dependencies: ggsci, methods, plyr,
        RcolorBrew, rlang, scales
      - we add the R package ggplotify from CRAN
  - The package now contains 321 tests and the coverage is now 90%
  - R functions of the packages
      - DEanalysisTimeAndGroup(): Correction when there are two time
        points by adding data.frame(X) as input of the function apply().
      - DATAplotExpression1Gene(): When data depends only on biological
        conditions, violin plots are plotted only if the number of
        individual per condition is >50.
      - For all the main functions, all results (plots too now) are now
        saved in the SummaryExperiment class object and can be accessed
        with the R function metadata (S4Vectors package).
      - PCAgraphics(): the 2D PCA graph with temporal links is now
        realized with ggplot2 and all 3D PCA graph is saved as ggplot2
        object with the R package ggplotify
      - MFUZZclustersNumber(): the plot is now realized with ggplot2
      - PCAgraphics(), PCAanalysis() and HCPCanalysis(): the input
        D3.mouvment is now called motion3D
      - Many functions have been split into several parts to make the
        code easier to read
  - Vignette (Running_analysis_with_MultiRNAflow.Rmd)
      - modification because of outputs and inputs modification
  - Vignette (MultiRNAflow_vignette-knitr.Rnw)
      - modification because of outputs and inputs modification
      - update of the vignette in order to answer comment of reviewers
        of Bioinformatics

                       Changes in version 0.99.9                        

Suggestions and remarks from a bioconductor team member

  - modification of outputs in order to replace list ouputs by SE class
    object
  - Vignette (Running_analysis_with_MultiRNAflow.Rmd)
      - modification because of ouputs modification
  - More unit tests (now 197 unit tests in 31 files), coverage = 60/100

                       Changes in version 0.99.8                        

Suggestions and remarks from a bioconductor team member

  - Correction of DESCRIPTION file
  - add a new function to improve inputs in others function
  - modification of R functions depending on previous inputs
  - Vignette (Running_analysis_with_MultiRNAflow.Rmd)
      - code-style to highlight (function, variable, package names)
      - keeping includegraphics only for the introduction part
  - More unit tests (now 45 unit tests in 25 files)
  - add the R file MultiRNAflow-package.R for man folder

                       Changes in version 0.99.7                        

Suggestions and remarks from a bioconductor team member

  - Correction of DESCRIPTION file
  - Vignette (Running_analysis_with_MultiRNAflow.Rmd)
      - code-style to highlight (function, variable, package names)
      - More details about the vignette
      - eval=FALSE replaced by eval=TRUE
  - More unit tests

                       Changes in version 0.99.6                        

Bug fixes

  - Necessary correction by the automated single package builder of
    bioconductor.org.

                       Changes in version 0.99.0                        

  - Added a NEWS.md file to track changes to the package.