Changes in version 1.1.4
+ Fixed bug in coveragePlot - github Issue 15: Previously the function cleaned
the beginning of each peptide sequence by gsub("^\[.\]\.([A-Z]+)\.\[.\]$",
"\1", .).  However, it is not always the case that the terminal amino acids are
surround by square brackets. I have put a more general regex in place that
removes everything up to the first '.' and everything after the last '.'. 

Changes in version 1.1.3
+ 'ImmunoOncology' added to BiocViews.

Changes in version 1.1.2
+ Updates to vignette to avoid build errors when attempting to connect to Uniprot

Changes in version 1.1.1
+ Fixed bug in maVolPlot - github Issue 12: Previously the 'selectedGenes'
argument used GeneSymbols to match genes to highlight in the plot. Not all
accessions are annotated with a GeneSymbol, and some GeneSymbols are linked to
more than one Accession. This could lead to situations where incorrect genes
were being highlighted due to duplicate entries or NAs. The function now accepts
and matches to accessions instead - this is now noted in the man pages.
+ Fixed bug in convertToMSnset - github Issue 11: The function previously threw
and error if the metadata was a tibble as it needs to set row names. The
function now tranforms the metadata object to a data frame.

Changes in version 1.1.0
+ First Bioconductor Devel (Bioconductor 3.9)

Changes in version 1.0.0
+ First Bioconductor Release (Bioconductor 3.8)

Changes in version 0.99.0
+ Initial version with the following functions implemented:       
    + convertToMSnset
    + summarizeIntensities
    + normalizeQuantiles
    + normalizeScaling
    + groupScaling
    + rowScaling
    + regressIntensity
    + computeDiffStats
    + getContrastResults
    + assignColours
    + intensityPlot
    + intensityBoxplot
    + peptideIntensityPlot
    + pcaPlot
    + maVolPlot
    + corrPlot
    + rliPlot
    + hierarchicalPlot
    + plotMeanVar
    + coveragePlot

  

