.extractTemplatesFromData
                        Helper function to extract template profiles
                        from user data
bootstrapIC50           Bootstrap IC50 Estimates and Confidence
                        Interval (ratio scale)
bootstrapIC50LogScale   Bootstrap IC50 Estimates and Confidence
                        Interval (log scale)
bootstrapIC50Precalculated
                        Bootstrap IC50 with pre-calculated ratios
calculatePeptideWeights
                        Calculate quality-based weights for peptide
                        measurements
calculateTurnoverRatios
                        Calculate turnover ratios from MSstats
                        FeatureLevelData
convertGroupToNumericDose
                        Convert MSstats GROUP labels to numeric dose in
                        nM and extract drug name
DIA_MSstats_Normalized
                        Example pre-processed DIA-MS dataset
doseResponseFit         Drug-protein interaction detection tested by
                        F-test (fitted curve vs average response)
fitIsotonicRegression   Fit Isotonic Regression Model
futureExperimentSimulation
                        Test future experimental design using simulated
                        data with user-defined or default templates
MSstatsPrepareDoseResponseFit
                        Prepare data for dose-response fitting with
                        isotonic regression
plot_tpr_power_curve    Visualize detection power across experimental
                        designs
plotHitRateMSstatsResponse
                        Plot hit rates by category
plotIsotonic            Plot Isotonic Regression Model
predictIC50             Predict IC50 (dose where response = target) for
                        each protein and drug
predictIC50Parallel     Parallel version of predictIC50 function
run_tpr_simulation      Simulate detection power across experimental
                        design configurations
simulateChemoProteinLevelNonParametric
                        Simulate chemoproteomics data at the protein
                        level - non-parametric approach
visualizeResponseProtein
                        Plot isotonic regression fit with optional IC50
                        for a single protein and drug
