Files in SafeQuant
A Toolbox for the Analysis of Proteomics Data
MD5
DESCRIPTION
README.md
NAMESPACE
inst/manuals/SafeQuant-man.pdf
inst/manuals/SafeQuant_UseCases.txt
inst/manuals/tsv_spreadsheet_help.docx
inst/manuals/tsv_spreadsheet_help.pdf
exec/installDependencies.R
exec/safeQuant.R
exec/filterLargeProgenesisPeptideFile.pl
exec/roxygenize.R
R/SafeQuantAnalysis.R
R/Graphics.R
R/IdentificationAnalysis.R
R/Parser.R
R/ExpressionAnalysis.R
R/UserOptions.R
R/TMT.R
man/isStrippedACs.Rd
man/plotPrecMassErrorVsScore.Rd
man/getPeptides.Rd
man/getNbPeptidesPerProtein.Rd
man/getGlobalNormFactors.Rd
man/getNbDetectablePeptides.Rd
man/plotPrecMassErrorDistrib.Rd
man/globalNormalize.Rd
man/getNbMisCleavages.Rd
man/getSignalPerCondition.Rd
man/rtNormalize.Rd
man/sqNormalize.Rd
man/getCV.Rd
man/removeOutliers.Rd
man/COLORS.Rd
man/getImpuritiesMatrix.Rd
man/plotNbValidDeFeaturesPerFDR.Rd
man/getLoocvFoldError.Rd
man/plotVolcano.Rd
man/getAAProteinCoordinates.Rd
man/getIntSumPerProtein.Rd
man/hClustHeatMap.Rd
man/safeQuantAnalysis.Rd
man/parseProgenesisPeptideMeasurementCsv.Rd
man/getRTNormFactors.Rd
man/expDesignTagToExpDesign.Rd
man/setNbSpectraPerProtein.Rd
man/stripACs.Rd
man/plotAdjustedVsNonAdjustedRatio.Rd
man/getScoreCutOff.Rd
man/option_list.Rd
man/cvBoxplot.Rd
man/parseScaffoldPTMReport.Rd
man/standardise.Rd
man/getMaxIndex.Rd
man/getTopX.Rd
man/parseScaffoldRawFile.Rd
man/plotExpDesign.Rd
man/plotAbsEstCalibrationCurve.Rd
man/getMotifX.Rd
man/getBaselineIntensity.Rd
man/getAllEBayes.Rd
man/createPairedExpDesign.Rd
man/addScaffoldPTMFAnnotations.Rd
man/perFeatureNormalization.Rd
man/getModifProteinCoordinates.Rd
man/barplotMSSignal.Rd
man/missinValueBarplot.Rd
man/parseMaxQuantProteinGroupTxt.Rd
man/getRatios.Rd
man/export.Rd
man/plotRTNorm.Rd
man/getAllCV.Rd
man/pairsAnnot.Rd
man/getMeanCenteredRange.Rd
man/isDecoy.Rd
man/parseProgenesisProteinCsv.Rd
man/createExpressionDataset.Rd
man/createExpDesign.Rd
man/plotQValueVsPValue.Rd
man/plotScoreDistrib.Rd
man/getUserOptions.Rd
man/plotXYDensity.Rd
man/getNbSpectraPerProtein.Rd
man/purityCorrectTMT.Rd
man/setNbPeptidesPerProtein.Rd
man/plotMSSignalDistributions.Rd
man/getIdLevelQvals.Rd
man/parseProgenesisFeatureCsv.Rd
man/isCon.Rd
man/getIBAQEset.Rd
man/plotROC.Rd
man/plotNbIdentificationsVsRT.Rd
man/maPlotSQ.Rd
man/getExpDesignProgenesisCsv.Rd
man/rollUp.Rd
man/addIdQvalues.Rd
man/plotRTNormSummary.Rd
man/plotIdScoreVsFDR.Rd
tests/testUserOptions.R
tests/testTMT.R
tests/testSafeQuantAnalysis.R
tests/testIdentificationAnalysis.R
tests/testParser.R
tests/initTestSession.R
tests/testExpressionAnalysis.R
tests/testGraphics.R
tests/runAllTest.R
tests/testData/progenesis_protein_export1.csv
tests/testData/maxquant_protein_groups.csv
tests/testData/progenesis_pep_measurement1.csv
tests/testData/scaffold_tmt10plex_calibMix_raw.xls
tests/testData/scaffold_tmt6plex_raw.xls
tests/testData/mouse_proteins.fasta
tests/testData/progenesis_feature_export1.csv
tests/testData/scaffold_tmt10plex_raw_phospho.xls
tests/testData/scaffold_tmt10plex_raw.xls
tests/testData/skyline_transition_results.csv
tests/testData/progenesis_pep_measurement_fractionated1.csv
tests/testData/scaffoldPtm_spectrum_report.xls
tests/testData/SQ_Results/SQ_Results.pdf
tests/testData/SQ_Results/SQ_Results_SQ_PARAMS.TXT
tests/testData/SQ_Results/SQ_Results_PROTEIN.tsv
