barplotPeptidesPerProtein | plot ranking metric vs peptide (per protein) barplot |
barplotPetideCountPerProtein | plot peptide count per protein |
createComplementaryIsotopeLibrary | Create complementary isotope (Arg, Lys H/L) spectral library |
createLibrarySpectrum | Parse spectrum framgment match information listed in MaxQuant... |
createSpectralLibrary | Create Spectral Library |
digestProteome | Get peptide candidates per protein |
getCMDLineOptions | Define and User Specified Command Line Options |
getEmpiricalIRT | Add iRT metric to data.frame |
getFragmentSequence | Get Fragment Sub Sequnece |
getIRTModel | Get linear model predicting iRT as a function retention time... |
getPeptides | Get Mz Shift of complementary peptide/fragment ion |
getPTMColors | assign colors to ptms |
getSearchedModifications | Get list of variable modifiections condsidered by MaxQuant |
getUserOptions | check and return User Specified Command Line Options |
parseMaxQuantMSMS | Parse MaxQuant msms.txt |
parseRange | Parse range in format 2:4 and return integer vector. Inthis... |
parseTargetsFile | Parse list of target peptides/proteins |
plotIRTCalibration | Plot IRT calibration curve |
proteotypicPeptideExport | # Export top X peptide per protein (ordered by... |
skylineExport | Write skyline compatible xls file |
spectroDiveExport | Write SpectroDive compatible xls file |
spectronautExport | Write Spectronaut compatible xls file |
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