| BTDR-package | Functions to access BUPID Top-Down results |
| bupid-class | Class bupid |
| bupid-print | Display BUPID results. |
| bupid-subset | Subset BUPID results. |
| bupid-summary | Summarize BUPID results. |
| fragment.coverage | Plot fragment coverage |
| fragment.mass.error | Plot mass errors for fragment assignments. |
| fragment.matched | Fragment assignment tables |
| read.bupid | Read BUPID results. |
| spectrum.plot | Plot spectra |
| write.mzid | Write results as mzIdentML. |
| xlinkpep | Crosslink peptide subset |
| xlinks | Crosslink results table |
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