SilacPeptideExperiment-class
                        SilacPeptideExperiment class
SilacPeptideExperiment-constructor
                        SilacPeptideExperiment constructor
SilacProteinExperiment-class
                        SilacProteinExperiment class
SilacProteinExperiment-constructor
                        SilacProteinExperiment constructor
SilacProteinPeptideExperiment-accessors
                        Accessors for the SilacProteinExperiment and
                        SilacPeptideExperiment classes
SilacProteomicsExperiment-accessors
                        Accessors for the SilacProteomicsExperiment
                        class
SilacProteomicsExperiment-class
                        SilacProteomicsExperiment class
SilacProteomicsExperiment-constructor
                        SilacProteomicsExperiment constructor
addMisscleavedPeptides
                        Add miss-cleaved peptide expression levels for
                        old isotope recycling estimation
barplotCounts           Number of detected features per sample
barplotTimeCoverage     Number of detected features per sample
buildLinkerDf           Constructs a linkerDf that can be used as input
                        when constructing a SilacProteomicsExperiment
calculateAIC            Calculates the Akaike Information Criteria
                        (AIC)
calculateIsotopeFraction
                        Calculates the incorporated isotope fraction
calculateIsotopeRatio   Ratio calculation
calculateOldIsotopePool
                        Estimates the fraction of old isotope for each
                        time point
compareAIC              Calculates the probability of each model from a
                        set of models.
filterByMissingTimepoints
                        Filter proteins/peptides by the amount of
                        measurements overtime
mefPE                   SilacProteomicsExperiment with pulsed silac
                        data from MEFs
merge                   Merge
mergeModelsLists        Merge several models lists.
modelTurnover           Estimate protein/peptide turnover
mostStable              Most stable proteins/peptides
plotDistributionAssay   Distribution of assay data per condition and
                        timepoint.
plotDistributionModel   Distribution of modelling output
plotIndividualModel     Fitted model(s) for a feature
recycleLightLysine      Data frame with miss cleaved peptides
                        quantifications from MaxQuant
scatterCompareAssays    Scatter plot of two conditions for each
                        timepoint of an assay.
scatterCompareModels    Scatter plot of two conditions for a model
                        metric.
upsetTimeCoverage       Number of detected features per sample
wormsPE                 ProteomicsExperiment with pulsed silac data
                        from C. elegans strains
