| .PAHD | An S4 class for ProteomicsAnnotationHubData objects |
| availableProteomicsAnnotationHubData | Get started with ProteomicsAnnotationHubData |
| identicalRemLoc | Are the remote and local instances identical |
| makeAnnotationHubMetadata | Make an AnnotationHubMeta resource |
| PAHD | Prepare data for inclusion into AnnotationHub |
| PAHD-class | An S4 class for ProteomicsAnnotationHubData objects |
| ProteomicsAnnotationHubData | Get started with ProteomicsAnnotationHubData |
| proteomicsAnnotationHubDataResources | Get started with ProteomicsAnnotationHubData |
| readPahdFiles | Reads one or multiple PAHD template files |
| writePahdTemplate | Write a ProteomicsAnnotationHubData template |