Boot_parallel           Parallel processing handling function
bootstrapS              Generate Bootstrap Samples
bootstrapSamples_limRots
                        Generate Stratified Bootstrap Samples for
                        limRots
calculateFalseDiscoveryRate
                        Calculate False Discovery Rate (FDR) Using
                        Permuted Values (Adjusted)
calOverlaps             Calculate Overlaps Between Observed and
                        Permuted Data
calOverlaps_slr         Calculate Overlaps for Single-Label Replicates
                        (SLR)
Check_meta_info         Check if meta info is correct
Check_SummarizedExperiment
                        Check if SummarizedExperiment or data is
                        correct
countLargerThan         Count Larger Permuted Values (Modified)
Limma_bootstrap         Perform Linear Modeling with Covariates using
                        Limma
Limma_fit               Perform Linear Modeling with Covariates using
                        Limma
Limma_permutating       Perform Permutation-Based Linear Modeling with
                        Covariates using Limma
LimROTS                 'LimROTS': A Hybrid Method Integrating
                        Empirical Bayes and Reproducibility-Optimized
                        Statistics for Robust Differential Expression
                        Analysis
Optimizing              Optimize Parameters Based on Overlap
                        Calculations
SanityChecK             Sanity Check for Input Data and Parameters
UPS1.Case4              Spectronaut and ScaffoldDIA UPS1 Spiked Dataset
                        case 4
