| applyThresholdCompartment | Apply thresholds to compartments | 
| applyThresholdNeighborhood | Apply thresholds to neighborhood classification | 
| calculateCoveredProtein | Evaluate marker protein coverage | 
| calRowMean | Compute the means of replicates | 
| candidateRelocatedProteins | Identify candidate relocated proteins | 
| compareCls | Compare exon and gene centric classifications | 
| computeThresholdCompartment | Probability threshold for compartment classification | 
| computeThresholdNeighborhood | Probability threshold for neighborhood classification | 
| convert2symbol | Convert identifier to gene symbol | 
| hcc827Ctrl | HCC827 Control Cell Line | 
| hcc827CtrlPSMCount | Minimum PSM Count in HCC827Ctrl Cell Line. | 
| hcc827exon | HCC827 Control Exon Cell Line | 
| hcc827GEF | Gefitinib treated HCC827 Cell Line | 
| hcc827GEFClass | Gefitinib treated HCC827 Cell Line Classification | 
| hcc827GefPSMCount | Minimum PSM Count in HCC827 Gefitinib Cell Line. | 
| loadData | Load the fractionated proteomics data | 
| markerProteins | Marker Proteins Source | 
| markerQualityControl | Evaluate the quality of the marker proteins | 
| mergeCls | Merge compartment and neighborhood classification | 
| mergeProbability | Merge compartment probabilities to neighborhood probabilities | 
| plotBarcode | Visualize the SubCellBarCode | 
| plotMultipleProtein | Visualization of multiple protein localizations | 
| replacePrediction | Replace compartment predictions to neighborhood predictions | 
| sankeyPlot | Sankey plot for condition-dependent protein relocalization | 
| sumProbability | Sum compartment test data probabilities to neighborhood probabilities | 
| svmClassification | Protein subcellular localization classification | 
| svmExternalData | Peptide/exon/transcript centric or PTM enriched classification | 
| tsneVisualization | Visualization of marker proteins by t-SNE map |