| .cleanRawPD | Clean raw Proteome Discoverer data |
| as.data.frame.MSstatsValidated | Convert output of converters to data.frame |
| as.data.table.MSstatsValidated | Convert output of converters to data.table |
| DIANNtoMSstatsFormat | Import Diann files |
| DIAUmpiretoMSstatsFormat | Import DIA-Umpire files |
| FragPipetoMSstatsFormat | Import FragPipe files |
| getInputFile | Get one of files contained in an instance of 'MSstatsInputFiles' class. |
| getInputFile-method | Get one of files contained in an instance of 'MSstatsInputFiles' class. |
| MaxQtoMSstatsFormat | Import MaxQuant files |
| MetamorpheusToMSstatsFormat | Import Metamorpheus files |
| MSstatsBalancedDesign | Creates balanced design by removing overlapping fractions and filling incomplete rows |
| MSstatsClean | Clean files generated by a signal processing tools. |
| MSstatsClean-method | Clean files generated by a signal processing tools. |
| MSstatsConvert | MSstatsConvert: An R Package to Convert Data from Mass Spectrometry Signal Processing Tools to MSstats Format |
| MSstatsImport | Import files from signal processing tools. |
| MSstatsLogsSettings | Set how MSstats will log information from data processing |
| MSstatsMakeAnnotation | Create annotation |
| MSstatsPreprocess | Preprocess outputs from MS signal processing tools for analysis with MSstats |
| MSstatsSaveSessionInfo | Save session information |
| OpenMStoMSstatsFormat | Import OpenMS files |
| OpenSWATHtoMSstatsFormat | Import OpenSWATH files |
| PDtoMSstatsFormat | Import Proteome Discoverer files |
| ProgenesistoMSstatsFormat | Import Progenesis files |
| ProteinProspectortoMSstatsTMTFormat | Generate MSstatsTMT required input format from Protein Prospector output |
| SkylinetoMSstatsFormat | Import Skyline files |
| SpectronauttoMSstatsFormat | Import Spectronaut files |