├── .Rbuildignore ├── .Rhistory ├── .gitignore ├── DESCRIPTION ├── MSLibrarian.Rproj ├── NAMESPACE ├── R ├── AddDeepLcRt.R ├── CIRT.R ├── CeBenchPlot.R ├── CheckMsFiles.R ├── CreateCalibrationLib.R ├── CreateSpectralLib.R ├── DigestProteins.R ├── ExportSpectraLib.R ├── FeatureFiltering.R ├── FilterLibPrecursors2.R ├── FilterPeptidesTmp.R ├── FilterPrego.R ├── FilterProteins.R ├── FilterTransitions.R ├── GetBestCe.R ├── GetLibPrecursors2.R ├── GetNoZeroIdx.R ├── GetPrecursors.R ├── GetSpectralDb.R ├── ImportCalibrationLib.R ├── ImportPrositLibrary.R ├── LoadPrositLibrary.R ├── MSLibrarianClass.R ├── MakeCalibrationLib.R ├── MakeDeepLcInputs.R ├── MakeMsms2.R ├── MakePredictionDb.R ├── MakePrositCsv.R ├── MakePseudoSpectra.R ├── MakeSpectraLib.R ├── MapDbEntries.R ├── MergePredictionDbs.R ├── ModSpectralLib.R ├── PrecursorBinning.R ├── ProcessCalibrationLib.R ├── ProcessPrositLibrary.R ├── ProteinFilter.R ├── ReadFasta.R ├── ReplaceRts.R ├── RunComet.R ├── RunDeepLc.R ├── RunDiaNN.R ├── RunMsConvert.R ├── RunMsFragger.R ├── RunProphets.R ├── RunSpectralMatch2.R └── prositAsSpectra.R ├── README.md ├── data └── cirt.RData ├── examples ├── demo_mslibr.Rmd └── demo_mslibr.html ├── man ├── CalibrationLibrary-class.Rd ├── add.deeplc.rt.Rd ├── ce.bench.plot.Rd ├── check.ms.files.Rd ├── cirt.Rd ├── create.calibration.lib.Rd ├── create.spectral.lib.Rd ├── digest.proteins.Rd ├── export.spectra.lib.Rd ├── feature.filtering.Rd ├── filter.lib.precursors2.Rd ├── filter.peptides.tmp.Rd ├── filter.prego.Rd ├── filter.proteins.Rd ├── filter.transitions.Rd ├── get.best.ce.Rd ├── get.lib.precursors2.Rd ├── get.no.zero.idx.Rd ├── get.precursors.Rd ├── get.spectral.db.Rd ├── import.calibration.lib.Rd ├── import.prosit.library.Rd ├── load.prosit.lib.Rd ├── make.calibration.lib.Rd ├── make.deeplc.inputs.Rd ├── make.msms2.Rd ├── make.prediction.db.Rd ├── make.prosit.csv.Rd ├── make.pseudo.spectra.Rd ├── make.spectra.lib.Rd ├── map.db.entries.Rd ├── merge.prediction.dbs.Rd ├── mod.spectral.lib.Rd ├── precursor.binning.Rd ├── process.calibration.lib.Rd ├── process.prosit.lib.Rd ├── prosit.as.spectra.Rd ├── protein.filter.Rd ├── read.fasta.Rd ├── replace.rts.Rd ├── run.comet.Rd ├── run.deeplc.Rd ├── run.diann.Rd ├── run.msconvert.Rd ├── run.msfragger.Rd ├── run.prophets.Rd └── run.spectral.match2.Rd └── params ├── comet_mslibrarian_default.params ├── diaumpire_se_mslibrarian_default.params ├── fragger_closed_mslibrarian_default.params ├── fragger_closed_mslibrarian_default_tmp.params ├── fragger_test1.params └── spectrast_create_mslibrarian_default.params /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarcIsak/MSLibrarian/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- 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