API for SafeQuant
A Toolbox for the Analysis of Proteomics Data
| Global functions | |
|---|---|
| COLORS | Man page |
| addIdQvalues | Man page |
| addScaffoldPTMFAnnotations | Man page |
| barplotMSSignal | Man page |
| createExpDesign | Man page |
| createExpressionDataset | Man page |
| createPairedExpDesign | Man page |
| cvBoxplot | Man page |
| expDesignTagToExpDesign | Man page |
| export | Man page |
| getAAProteinCoordinates | Man page |
| getAllCV | Man page |
| getAllEBayes | Man page |
| getBaselineIntensity | Man page |
| getCV | Man page |
| getExpDesignProgenesisCsv | Man page |
| getGlobalNormFactors | Man page |
| getIBAQEset | Man page |
| getIdLevelQvals | Man page |
| getImpuritiesMatrix | Man page |
| getIntSumPerProtein | Man page |
| getLoocvFoldError | Man page |
| getMaxIndex | Man page |
| getMeanCenteredRange | Man page |
| getModifProteinCoordinates | Man page |
| getMotifX | Man page |
| getNbDetectablePeptides | Man page |
| getNbMisCleavages | Man page |
| getNbPeptidesPerProtein | Man page |
| getNbSpectraPerProtein | Man page |
| getPeptides | Man page |
| getRTNormFactors | Man page |
| getRatios | Man page |
| getScoreCutOff | Man page |
| getSignalPerCondition | Man page |
| getTopX | Man page |
| getUserOptions | Man page |
| globalNormalize | Man page |
| hClustHeatMap | Man page |
| isCon | Man page |
| isDecoy | Man page |
| isStrippedACs | Man page |
| maPlotSQ | Man page |
| missinValueBarplot | Man page |
| option_list | Man page |
| pairsAnnot | Man page |
| parseMaxQuantProteinGroupTxt | Man page |
| parseProgenesisFeatureCsv | Man page |
| parseProgenesisPeptideMeasurementCsv | Man page |
| parseProgenesisProteinCsv | Man page |
| parseScaffoldPTMReport | Man page |
| parseScaffoldRawFile | Man page |
| perFeatureNormalization | Man page |
| plotAbsEstCalibrationCurve | Man page |
| plotAdjustedVsNonAdjustedRatio | Man page |
| plotExpDesign | Man page |
| plotIdScoreVsFDR | Man page |
| plotMSSignalDistributions | Man page |
| plotNbIdentificationsVsRT | Man page |
| plotNbValidDeFeaturesPerFDR | Man page |
| plotPrecMassErrorDistrib | Man page |
| plotPrecMassErrorVsScore | Man page |
| plotQValueVsPValue | Man page |
| plotROC | Man page |
| plotRTNorm | Man page |
| plotRTNormSummary | Man page |
| plotScoreDistrib | Man page |
| plotVolcano | Man page |
| plotXYDensity | Man page |
| purityCorrectTMT | Man page |
| removeOutliers | Man page |
| rollUp | Man page |
| rtNormalize | Man page |
| safeQuantAnalysis | Man page |
| setNbPeptidesPerProtein | Man page |
| setNbSpectraPerProtein | Man page |
| sqNormalize | Man page |
| standardise | Man page |
| stripACs | Man page |
