Package: MSstatsConvert 1.17.0
Mateusz Staniak
MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.
Authors:
MSstatsConvert_1.17.0.tar.gz
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MSstatsConvert.pdf |MSstatsConvert.html✨
MSstatsConvert/json (API)
NEWS
| # Install 'MSstatsConvert' in R: |
| install.packages('MSstatsConvert', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:MSstatsConvert-1.15.6(bioc 3.20)MSstatsConvert-1.14.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
massspectrometryproteomicssoftwaredataimportqualitycontrol
Last updated 22 days agofrom:12a3b89ff1. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 30 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 30 2024 |
| R-4.4-mac | WARNING | Oct 30 2024 |
| R-4.3-win | WARNING | Oct 30 2024 |
| R-4.3-mac | WARNING | Oct 30 2024 |
Exports:DIANNtoMSstatsFormatDIAUmpiretoMSstatsFormatFragPipetoMSstatsFormatgetDataTypegetInputFileMaxQtoMSstatsFormatMetamorpheusToMSstatsFormatMSstatsBalancedDesignMSstatsCleanMSstatsImportMSstatsLogsSettingsMSstatsMakeAnnotationMSstatsPreprocessMSstatsSaveSessionInfoOpenMStoMSstatsFormatOpenSWATHtoMSstatsFormatPDtoMSstatsFormatProgenesistoMSstatsFormatProteinProspectortoMSstatsTMTFormatSkylinetoMSstatsFormatSpectronauttoMSstatsFormat
Dependencies:backportscheckmatedata.tablelog4rstringi
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clean raw Proteome Discoverer data | .cleanRawPD |
| Helper method to validate input has necessary columns | .validatePDTMTInputColumns |
| Convert output of converters to data.frame | as.data.frame.MSstatsValidated |
| Convert output of converters to data.table | as.data.table.MSstatsValidated |
| Import Diann files | DIANNtoMSstatsFormat |
| Import DIA-Umpire files | DIAUmpiretoMSstatsFormat |
| Import FragPipe files | FragPipetoMSstatsFormat |
| Get one of files contained in an instance of 'MSstatsInputFiles' class. | getInputFile getInputFile,MSstatsInputFiles-method getInputFile,MSstatsPhilosopherFiles-method |
| Import MaxQuant files | MaxQtoMSstatsFormat |
| Import Metamorpheus files | MetamorpheusToMSstatsFormat |
| Creates balanced design by removing overlapping fractions and filling incomplete rows | MSstatsBalancedDesign |
| Clean files generated by a signal processing tools. | MSstatsClean MSstatsClean,MSstatsDIANNFiles-method MSstatsClean,MSstatsDIAUmpireFiles-method MSstatsClean,MSstatsMaxQuantFiles-method MSstatsClean,MSstatsMetamorpheusFiles-method MSstatsClean,MSstatsOpenMSFiles-method MSstatsClean,MSstatsOpenSWATHFiles-method MSstatsClean,MSstatsPhilosopherFiles-method MSstatsClean,MSstatsProgenesisFiles-method MSstatsClean,MSstatsProteinProspectorFiles-method MSstatsClean,MSstatsProteomeDiscovererFiles-method MSstatsClean,MSstatsSkylineFiles-method MSstatsClean,MSstatsSpectroMineFiles-method MSstatsClean,MSstatsSpectronautFiles-method |
| MSstatsConvert: An R Package to Convert Data from Mass Spectrometry Signal Processing Tools to MSstats Format | MSstatsConvert-package MSstatsConvert |
| Import files from signal processing tools. | MSstatsImport |
| Set how MSstats will log information from data processing | MSstatsLogsSettings |
| Create annotation | MSstatsMakeAnnotation |
| Preprocess outputs from MS signal processing tools for analysis with MSstats | MSstatsPreprocess |
| Save session information | MSstatsSaveSessionInfo |
| Import OpenMS files | OpenMStoMSstatsFormat |
| Import OpenSWATH files | OpenSWATHtoMSstatsFormat |
| Import Proteome Discoverer files | PDtoMSstatsFormat |
| Import Progenesis files | ProgenesistoMSstatsFormat |
| Generate MSstatsTMT required input format from Protein Prospector output | ProteinProspectortoMSstatsTMTFormat |
| Import Skyline files | SkylinetoMSstatsFormat |
| Import Spectronaut files | SpectronauttoMSstatsFormat |
