addIdQvalues | Add identification leve q-values to ExpressionSet (calculated... |
addScaffoldPTMFAnnotations | Add scaffold ptm annotaitons to tmt experiment |
barplotMSSignal | Barplot of ms-signal per column |
COLORS | color vector |
createExpDesign | Create Experimental Design |
createExpressionDataset | Create ExpressionSet object |
createPairedExpDesign | Create Paired Expdesign |
cvBoxplot | C.V. boxplot |
expDesignTagToExpDesign | Create experimental design data.frame from user input string |
export | Export content of safeQuantAnalysis object |
getAAProteinCoordinates | Get amino acid coordinates on protein |
getAllCV | Calculate Coefficiant of Variance per feature (Relative... |
getAllEBayes | Perform statistical test (mderated t-test), comparing all... |
getBaselineIntensity | Get signal at zscore x (x standard deviations below mean) |
getCV | Calculate Coefficiant of Variance per feature (Relative... |
getExpDesignProgenesisCsv | Parse Experimental Design from Progenesis Csv Export |
getGlobalNormFactors | Get normalization factors. calculated as summed/median signal... |
getIBAQEset | Calculate intensity-based absolute-protein-quantification... |
getIdLevelQvals | Calculates identification level q-values based on... |
getImpuritiesMatrix | Get Thermo TMT impurity matrix |
getIntSumPerProtein | Sum up raw intensities per protein and channel. keep track of... |
getLoocvFoldError | Leave-One-Out Cross Validate Qunatification Model |
getMaxIndex | get index of max in vecotr of numeric values |
getMeanCenteredRange | Get modification coordinates on protein |
getModifProteinCoordinates | Get modification coordinates on protein |
getMotifX | Create motif-x peptide annotation |
getNbDetectablePeptides | Get number peptides passing defined length criteria |
getNbMisCleavages | Get number of mis-cleavages perp peptide |
getNbPeptidesPerProtein | Get number of peptides per protein |
getNbSpectraPerProtein | Get number of spectra per protein |
getPeptides | Digest protein |
getRatios | Calculate ratios, comparing all case to control |
getRTNormFactors | Get retentiontime base normalization factors |
getScoreCutOff | Get score cutoff for a given fdr cut-off |
getSignalPerCondition | Summarize replicate signal per condition (min) |
getTopX | Calculate Mean of X most intense features |
getUserOptions | Read User Specified Command Line Options |
globalNormalize | Normalize, Norm factors calculated as median signal per run... |
hClustHeatMap | Hierarchical clustering heat map, cluster by runs intensity,... |
isCon | Check if protein is a contaminant entry |
isDecoy | Check if protein is a decoy entry |
isStrippedACs | Check if ACs are in "non-stripped" uniprot format e.g.... |
maPlotSQ | ma-plot |
missinValueBarplot | Plot Percentage of Features with with missing values |
option_list | Command Line Option List |
pairsAnnot | Plot lower triangle Pearsons R^2. Diagonal text, upper... |
parseMaxQuantProteinGroupTxt | Parse MaxQuant Protein Group Txt |
parseProgenesisFeatureCsv | Parse Progenesis Feature Csv Export |
parseProgenesisPeptideMeasurementCsv | Parse Progenesis Peptide Measurement Csv Export |
parseProgenesisProteinCsv | Parse Progenesis Protein Csv |
parseScaffoldPTMReport | Parse scaffold PTM Spectrum Report |
parseScaffoldRawFile | Parse scaffold output .xls file (RAW export) |
perFeatureNormalization | Per Feature Normalization |
plotAbsEstCalibrationCurve | Plot absolut Estimation calibration Curve |
plotAdjustedVsNonAdjustedRatio | Plot adjusted tmt ratios vs original ratios |
plotExpDesign | Display experimental design, high-lighting the control... |
plotIdScoreVsFDR | Plot FDR vs. identification score |
plotMSSignalDistributions | Plot ms.signal distributions |
plotNbIdentificationsVsRT | Plot the number of identified Features per Reteintion Time... |
plotNbValidDeFeaturesPerFDR | Plot Total Number of diffrentially Abundant Features... |
plotPrecMassErrorDistrib | Plot Precursor Mass Error Distribution |
plotPrecMassErrorVsScore | Plot precursorMass error v.s score highlighting decoy and... |
plotQValueVsPValue | Plot qValue vs pValue |
plotROC | Plot Number of Identifications vs. FDR |
plotRTNorm | Plot all retention time profile overalying ratios |
plotRTNormSummary | Plot all retention time normalization profiles |
plotScoreDistrib | Plot identifications target decoy distribution |
plotVolcano | Plots volcano, data points colored by max cv of the 2... |
plotXYDensity | Scatter plot with density coloring |
purityCorrectTMT | Correct channel intensities based on Reporter ion Isotopic... |
removeOutliers | Set value to NA if it deviatves with more than 1.5 * IQR from... |
rollUp | Roll up feature intensites per unique colum combination |
rtNormalize | Normalization data per retention time bin |
safeQuantAnalysis | safeQunat s3 class |
setNbPeptidesPerProtein | Set nbPeptides coulmn of featureData |
setNbSpectraPerProtein | Set nbPeptides coulmn of featureData |
sqNormalize | Normalize |
standardise | Standardise data |
stripACs | strip uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE" -> Q8CHJ2 |
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