| AggLimmaWorkflow | Aggregation-based LIMMA workflow |
| AggPeps | Aggregate peptide abundance values |
| CompPepSetTest | Competitive peptide set test |
| CompPepSetTestWorkflow | Competitive Peptide Set Test Workflow |
| EnframeContrastsRes | Enframe result of LIMMA analysis |
| EstimInterPepCor | Estimation of inter-peptide correlation |
| FitContrasts | Empirical Bayes moderated t-test |
| FitLmerBySample | Fit a linear mixed model |
| RobustReg | Robust Regression |
| SelfContPepSetTestWorkflow | Self-contained Peptide Set Test Workflow |
| TTestwCor | Two-sample t-test accounting for inter-peptide correlation |