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| aaDist | Position Independent Amino Acid Distributions |
| aaStruct | Positional Amino Acid Composition Calculations |
| Attrib | Calculate Peptide Length and Charge Attributes |
| Dups | Average duplicated peptides from a VDAP dataset |
| genPep | Peptide generator based on the output of functions 'vComp' or 'vMotif' |
| hitSel | Signal Based Hits Selection for VDAP |
| KdA | Peptide Dissociation Rate Constant (Kd) Calculations |
| lcScan | Signal or Kd Distributions separated by Length/Charge attributes |
| QCKd | Quality Control of Peptides Based on Reproducibility and Kd |
| QCon | Subsetting for VDAP function QCKd |
| resSep | Select Peptides with the Specified Amino Acid Residue(s) at an Indicated Position |
| vComp | Amino Acid Disbutions by Position at Various Length/Charge |
| vComp.l | Amino Acid Disbutions by Position at Various Length/Charge |
| vComp.lc | Amino Acid Disbutions by Position at Various Length/Charge |
| vFormat | Length/Charge/Kd Peptide Calculations and File Assembly |
| vMotif | Generate Signal Weighted Amino Acid Heat Maps by Position |
| vMotif.l | Generate Signal Weighted Amino Acid Heat Maps by Position |
| vMotif.lc | Generate Signal Weighted Amino Acid Heat Maps by Position |
| vSep | Select Peptides of a Particular Length/Charge Combination |