├── DESCRIPTION ├── NAMESPACE ├── R ├── completeMomentsON.R ├── dpc.R ├── dpcCN.R ├── dpcDE.R ├── dpcImpute.R ├── dpcImputeHyperparam.R ├── dpcON.R ├── dpcQuant.R ├── dpcquantHyperparam.R ├── dztbinom.R ├── estimateDPCIntercept.R ├── filterCompoundProteins.R ├── filterNonProteotypicPeptides.R ├── filterSingletonPeptides.R ├── fitZTLogit.R ├── imputeByExpTilt.R ├── peptides2ProteinBFGS.R ├── peptides2ProteinNewton.R ├── peptides2ProteinWithoutNAs.R ├── peptides2Proteins.R ├── plotDPC.R ├── plotMDSUsingSEs.R ├── plotPeptides.R ├── plotProtein.R ├── proteinResVarFromCompletePeptideData.R ├── pztbinomSameSizeLogitPBothTails.R ├── readDIANN.R ├── readFragPipe.R ├── readMaxQuant.R ├── readSpectronaut.R ├── removeNARows.R ├── simCompleteDataON.R ├── simProteinDataSet.R └── voomaLmFitWithImputation.R ├── README.md ├── inst ├── CITATION └── NEWS.Rd ├── man ├── completeMomentsON.Rd ├── dpc.Rd ├── dpcCN.Rd ├── dpcDE.Rd ├── dpcQuant.Rd ├── dpcquantHyperparam.Rd ├── dtbinom.Rd ├── estimateDPCIntercept.Rd ├── filterCompoundProteins.Rd ├── fitZTLogit.Rd ├── imputeByExpTilt.Rd ├── limpa-package.Rd ├── observedMomentsCN.Rd ├── peptide2Protein.Rd ├── peptide2Proteins.Rd ├── plotDPC.Rd ├── plotMDSUsingSEs.Rd ├── plotPeptides.Rd ├── plotProtein.Rd ├── proteinResVarFromCompletePeptideData.Rd ├── pztbinomSameSizeLogitPBothTails.Rd ├── readDIANN.Rd ├── readFragPipe.Rd ├── readMaxQuant.Rd ├── readSpectronaut.Rd ├── removeNARows.Rd ├── simCompleteDataON.Rd ├── simProteinDataSet.Rd └── voomaLmFitWithImputation.Rd ├── tests ├── limpa-Tests.R └── limpa-Tests.Rout.save └── vignettes └── limpa.Rmd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SmythLab/limpa/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 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