Man pages for MarcIsak/MSLibrarian
What the Package Does (One Line, Title Case)
| add.deeplc.rt | Adds DeepLC retention times to the predicted Prosit library |
| CalibrationLibrary-class | Class definition of a MSLibrarian object |
| ce.bench.plot | Makes a plot over the best dot products and optimal collision... |
| check.ms.files | Checks if DIA files are valid |
| cirt | Conserved iRT peptides |
| create.calibration.lib | Creates a calibration library from a set of DIA files and a... |
| create.spectral.lib | Creates a spectral library with intensities and retention... |
| digest.proteins | Returns peptide sequences resulting from protein digestion... |
| export.spectra.lib | Creates a generic spectral library from predicted data, which... |
| feature.filtering | Performs a filtering of MSLibrarian-predicted libraries based... |
| filter.lib.precursors2 | Filters slot PrecursorData$Consensus, and returns the... |
| filter.peptides.tmp | Filters peptide sequences based on amino acid length |
| filter.prego | Filter spectral library based on top N high responding... |
| filter.proteins | Subsets a spectral library based on a selection of protein... |
| filter.transitions | Performs transition filtering of a library, either based on... |
| get.best.ce | Extract the optimal collision energy based on peptide length,... |
| get.lib.precursors2 | Extracts the unique precursor information from an imported... |
| get.no.zero.idx | Get row indices for transitions in predicted spectral... |
| get.precursors | Generates precursor m/z values for a filtered list of... |
| get.spectral.db | Downloads a Spectral Warehouse SQLite database with... |
| import.calibration.lib | Creates a Spectrast Library object, and imports a Spectrast... |
| import.prosit.library | Loads a predicted spectral library and extracts the relevant... |
| load.prosit.lib | Loads a processed Prosit Library file into a MSLibrarian... |
| make.calibration.lib | Create a calibration library in OpenSwath format (TSV) |
| make.deeplc.inputs | Creates input csv files for retention time predictions in... |
| make.msms2 | Adds MS/MS information from Spectral library file into a... |
| make.prediction.db | Creates a predicted spectral library database |
| make.prosit.csv | Generates a CSV file with precursor information, to be used... |
| make.pseudo.spectra | Creates pseudo DDA spectra f |
| make.spectra.lib | Create a predicted spectral library |
| map.db.entries | Map entries in the predicted spectral library database to the... |
| merge.prediction.dbs | Merges prediction databases allowing for creation of... |
| mod.spectral.lib | Modifies and filters a spectral library on protein, peptide,... |
| precursor.binning | Bin precursors based on number cutoff |
| process.calibration.lib | Creates and processes a calibration library object |
| process.prosit.lib | Loads a predicted spectral library and extracts the relevant... |
| prosit.as.spectra | Make part of prosit library file into Spectrum2 objects... |
| protein.filter | Subsets an input spectral library based on protein IDs |
| read.fasta | Reads a fasta file of AA sequences and stores the information... |
| replace.rts | Replaces the retention times for an input spectral library |
| run.comet | Runs the database search engine Comet on input spectral files |
| run.deeplc | Runs DeepLC to predict retention times for a set of peptides |
| run.diann | Runs a DIA-NN analysis of the selected DIA-file and input... |
| run.msconvert | Converts MS RAW files to desired output format using... |
| run.msfragger | Runs the MSFragger database search tool on pseudo-DDA MS/MS... |
| run.prophets | Runs PeptideProphet and iProphet on input Comet search engine... |
| run.spectral.match2 | Runs spectral comparisons between experimental spectra in the... |
