Changes in version 1.7.1                        

  - R functions of the packages
      - myYlabelNorm() (included in the R function
        DATAplotExpressionGenes()): there were an error when the RPKM
        normalization were used.
      - GSEAQuickAnalysis():
          - replace size aesthetic by linewidth because : Using size
            aesthetic for lines was deprecated in ggplot2 3.4.0.
          - correction errors: print(gManhattan) to
            print(gproList$gManhattan)
      - MFUZZclustersNumber(): slight modification for correcting one
        warning "Removed 1 row containing missing values or values
        outside the scale range (geom_point())."
      - DEplotBarplot(): in the section "Examples", we replace
        c("Spe.Pos", "Spe.Neg", "Other") by c("UpRegulated",
        "DownRegulated", "Other").
      - DEplotBarplotFacetGrid(): in the section "Examples", we add
        Melt.Dat.2 <- stats::aggregate(Nb.Spe.DE~., data=Melt.Dat.2,
        sum) so Melt.Dat.2 is more representative of the data used by
        our function. We also modify the function to prevent recent
        warnings from ggplot2 (.data[["<col_names>"]]).
  - Vignette (MultiRNAflow_vignette-knitr.Rnw)
      - We add our publication from Bioinformatics
      - we correct new errors produced by latex output
          - problem with the input max.level of the function str()
          - we correct the following new error 'Illegal parameter number
            in definition of \NewValue'
          - we use '\printbibliography' and '\addbibresource' in the
            preamble for the 'cleaner' biblatex interface.

                       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.