| bootstrapS | Generate Bootstrap Samples |
| bootstrapSamples_limRots | Generate Stratified Bootstrap Samples for limRots |
| Boot_parallel | Parallel processing handling function |
| 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 |