├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── func.R ├── live.R └── uniprot.R ├── README.md ├── man ├── RAS.Rd ├── aggregateHifly.Rd ├── aggregateMedian.Rd ├── aggregateSum.Rd ├── allProteinTable.Rd ├── allowedUniProtColumns.Rd ├── annotateProteins.Rd ├── evidenceColumns.Rd ├── fetchFromUniProt.Rd ├── goodData.Rd ├── intensityStats.Rd ├── jaccardSimilarity.Rd ├── jitterPlot.Rd ├── limmaDE.Rd ├── limmaRatioDE.Rd ├── makePeptideTable.Rd ├── makeProteinTable.Rd ├── measureColumns.Rd ├── normalizeData.Rd ├── normalizeMedian.Rd ├── normalizeTMT.Rd ├── parameterString.Rd ├── plotClustering.Rd ├── plotCount.Rd ├── plotDetectionSimilarity.Rd ├── plotDistanceMatrix.Rd ├── plotFID.Rd ├── plotFID_live.Rd ├── plotIntensities.Rd ├── plotMV.Rd ├── plotPCA.Rd ├── plotPdist.Rd ├── plotProtPeptides.Rd ├── plotSampleDistributions.Rd ├── plotVolcano.Rd ├── plotVolcano_live.Rd ├── proteinColumns.Rd ├── proteinInfo.Rd ├── proteusData.Rd ├── readColumnNames.Rd ├── readEvidenceFile.Rd ├── readProteinGroups.Rd ├── replicateTable.Rd ├── significanceTable.Rd ├── summary.proteusData.Rd └── tryQuery.Rd ├── proteus.Rproj ├── tests ├── testdata │ ├── data_makePeptide_evi.txt │ └── data_makePeptide_meta.txt ├── testthat.R └── testthat │ ├── test_jaccardSimilarity.R │ ├── test_makePeptideTable.R │ └── test_makeProtein.R └── vignettes ├── SILAC.Rmd ├── TMT.Rmd └── proteus.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bartongroup/Proteus/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bartongroup/Proteus/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: 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