DDARawData              Example dataset from a label-free DDA, a
                        controlled spike-in experiment.
DDARawData.Skyline      Example dataset from a label-free DDA, a
                        controlled spike-in experiment, processed by
                        Skyline.
DIARawData              Example dataset from a label-free DIA, a group
                        comparison study of S.Pyogenes.
DIAUmpiretoMSstatsFormat
                        Generate MSstats required input format for
                        DIA-Umpire output
MSstats-package         Tools for protein significance analysis in
                        DDA,SRM and DIA proteomic experiments for
                        label-free workflows or workflows with stable
                        isotope labeled reference
MaxQtoMSstatsFormat     Generate MSstats required input format for
                        MaxQuant output
OpenMStoMSstatsFormat   Generate MSstats required input format for
                        OpenMS output
OpenSWATHtoMSstatsFormat
                        Generate MSstats required input format for
                        OpenSWATH output
PDtoMSstatsFormat       Generate MSstats required input format for
                        Proteome discoverer output
ProgenesistoMSstatsFormat
                        Generate MSstats required input format for
                        Progenesis output
SRMRawData              Example dataset from a SRM experiment with
                        stable isotope labeled reference of a time
                        course yeast study
SkylinetoMSstatsFormat
                        Generate MSstats required input format for
                        Skyline output
SpectronauttoMSstatsFormat
                        Generate MSstats required input format for
                        Spectronaut output
SpikeInDataLinear       Example dataset from an MRM spike-in experiment
                        with a linear behavior
SpikeInDataNonLinear    Example dataset from an MRM spike-in experiment
                        with a nonlinear behavior
dataProcess             Data pre-processing and quality control of MS
                        runs of raw data
dataProcessPlots        Visualization for explanatory data analysis
designSampleSize        Planning future experimental designs of
                        Selected Reaction Monitoring (SRM),
                        Data-Dependent Acquisition (DDA or shotgun),
                        and Data-Independent Acquisition (DIA or
                        SWATH-MS) experiments in sample size
                        calculation
designSampleSizeClassification
                        Estimate the optimal size of training data for
                        classification problem
designSampleSizeClassificationPlots
                        Visualization for sample size calculation in
                        classification problem
designSampleSizePlots   Visualization for sample size calculation
groupComparison         Finding differentially abundant proteins across
                        conditions in targeted Selected Reaction
                        Monitoring (SRM), Data-Dependent Acquisition
                        (DDA or shotgun), and Data-Independent
                        Acquisition (DIA or SWATH-MS) experiment
groupComparisonPlots    Visualization for model-based analysis and
                        summarizing differentially abundant proteins
linear_quantlim         Calculation of the LOB and LOD with a linear
                        fit
modelBasedQCPlots       Visualization for model-based quality control
                        in fitting model
nonlinear_quantlim      Calculation of the LOB and LOD with a nonlinear
                        fit
plot_quantlim           Plot of the curve used to calculate LOB and LOD
quantification          Protein sample quantification or group
                        quantification
