ER_ARID1A_KO_MCF7       ER_ARID1A_KO_MCF7 dataset
IRSnorm                 Batch Correction by Internal Reference Scale
assignColours           Assigns colours to samples in groups
computeDiffStats        Compute differential statistics
convertToMSnset         Converts proteomics TMT intensity data to
                        MSnSet
corrPlot                Correlation plot
coveragePlot            Plot peptide sequence coverage
exp2_Xlink              exp2_Xlink dataset
exp3_OHT_ESR1           exp3_OHT_ESR1 dataset
getContrastResults      Get differential statistics results
groupScaling            Normalization by scaling within group
hierarchicalPlot        Hierarchical clustering plot
human_anno              human_anno dataset
intensityBoxplot        Intensity Distribution boxplot
intensityPlot           Intensity Distribution Plot
maVolPlot               MA or Volcano Plot
mergePeptides           Merge identical peptides intensities
mouse_anno              mouse_anno dataset
normalizeQuantiles      Quantile normalization
normalizeScaling        Normalization by scaling
pcaPlot                 PCA plot
peptideIntensityPlot    Plot peptide intensities
plotMeanVar             Mean variance plot
qPLEXanalyzer-package   Tools for qPLEX-RIME data analysis
regressIntensity        Regression based analysis
rliPlot                 Relative log intensity plot
rowScaling              Normalization by scaling peptide/protein
                        intensity across all samples
summarizeIntensities    Summarizes peptides intensities to proteins
