Changes in version 1.3.3                        

  - Removed unused dependency.

                        Changes in version 1.3.2                        

  - Reporthing the fixed Modifications if the mqpar.xml is present.

                        Changes in version 1.3.1                        

  - Added median to the PlotAndromedaScore().
  - Remove warnings from the vignettes.
  - Now MQmetrics can read the mqpar.xml file. This one must be located
    on the same directory as the combined folder.
  - Reporting the number of threads used by MaxQuant if found the
    mqpar.xml file.

                        Changes in version 1.1.8                        

  - Fixed test that was resulting in error duet to version 1.1.6 updated
    way to read the files.

                        Changes in version 1.1.7                        

  - Removed parentheses from the news that was causing issues in
    Bioconductor.

                        Changes in version 1.1.6                        

  - Bug fixed: If a table was missing, the report was not generated.

                        Changes in version 1.1.5                        

  - The plot generated by PlotPTM() will now indicate (in the legend
    title) whether the Post-Translational modifications have been
    aggregated or not as a result of the parameter aggregate_PTMs.

  - The function PlotPeptidesIdentified() and PlotProteinsIdentified()
    now return a plot containing Missing Values, Frequency of Identified
    by Match Between Runs and Frequency of identified by MS/MS. With
    this, the funciton PlotIdentificationType() becomes obsolete.

  - The function PlotProteinCoverage() now can take as input multiple
    UniprotID in a vector format.

  - The function PlotPTMAcrossSamples() now can take as input multiple
    PTM_of_Interest in a vector format.

  - Change in the function make_MQCombined() to read faster the tables
    and reducing the overall time required to generate a report.

                        Changes in version 1.1.4                        

  - The function PlotProteinCoverage() now reports the coverage
    individually in each plot rather than the total protein coverage.

  - MQmetrics now is adapted to MaxQuant v.2.x, since the column names
    are different than in MaxQuant v.1.x. MQmetrics will detect the
    MaxQuant version used and read the columns accordingly.

  - Enhanced error message in PlotiRT() and PlotiRTScore() when irt
    peptides are note found. Enhanced error message for
    PlotProteinCoverage() when the UniprotID is not found.

                        Changes in version 1.1.3                        

  - Added new function PlotPTMAcrossSamples(), it takes as input one PTM
    of interest and shows its intensities across the samples. This
    function is similar to PlotPTM() but in more detail.
  - In the function PlotPTM() a parameter combine_same_residue_ptms has
    been added. It combines multiple PTMs happening in the same residue
    such as: Dimethyl (KR), Trimethyl (KR).

                        Changes in version 1.1.2                        

  - Fixed units of time MaxQuantAnalysisInfo() when experiment lasting
    longer than a day.
  - Added new line to MaxQuantAnalyssInfo() showing when the experiment
    ended.
  - Improved aesthethics in the plots from PlotCombinedDynamicRange()
    and PlotAllDynamicRange().

                        Changes in version 1.1.1                        

  - Added pagination to PlotiRT() and PlotiRTScore().
  - Updated vignette style to Bioconductor's.
  - Improved aesthethics of PlotProteinOverlap() and PlotPCA().

                        Changes in version 1.0.0                        

  - The function generateReport() now takes the parameter
    name_output_file to name the output pdf file.
  - Added information regarding peptides, and peptides/protein ratio in
    report tables.
  - Added the function PlotProteinPeptideRatio() to visualize a
    comparison between the proteins identified and the ratio
    Peptide/Proteins among Experiments.

                       Changes in version 0.99.3                        

  - Functions now use a general input resulting from make_MQCombined().
  - Shortened lines in the code.
  - Usage of seq_len rather than 1: ...
  - Usage of ultiples of 4 spaces for line indents.
  - Removed LazyData: TRUE.

                       Changes in version 0.99.2                        

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