API for UCLouvain-CBIO/scp
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
| Global functions | |
|---|---|
| .adaptModel | Source code |
| .addEigenArrows | Source code |
| .addPcaToList | Source code |
| .centerNumericalVariables | Source code |
| .checkAnnotations | Source code |
| .checkContrasts | Source code |
| .checkExperimentalDesignRank | Source code |
| .checkExplanatoryVariables | Source code |
| .checkInputIndex | Source code |
| .checkModelElement | Source code |
| .checkModelName | Source code |
| .checkPCAResults | Source code |
| .checkScpModelFormula | Source code |
| .coefficientToEstimates | Source code |
| .componentsToTable | Source code |
| .computeCumulativeSensitivityCurve | Source code |
| .computeEffectSS | Source code |
| .computeJaccardIndex | Source code |
| .computeMissingValueMetrics | Source code |
| .computeModelEffect | Source code |
| .computeModelEffects | Source code |
| .computeResidualSS | Source code |
| .computeSumsOfSquares | Source code |
| .computeTTest | Source code |
| .computeTotalSS | Source code |
| .contrastToEstimates | Source code |
| .createAxisLabelsForPCA | Source code |
| .defaultModelName | Source code |
| .dropConstantVariables | Source code |
| .estimateModel | Source code |
| .explainedVarianceDenominator | Source code |
| .filterDifferentialData | Source code |
| .filterPlot | Source code |
| .filterSubtitle | Source code |
| .filterVarianceData | Source code |
| .fitRidge | Source code |
| .fitScpModel | Source code |
| .formatCategoricalVariables | Source code |
| .formatEigenVectors | Source code |
| .formatPcaList | Source code |
| .gatherVarianceData | Source code |
| .getDetectionMatrix | Source code |
| .getPcaFunction | Source code |
| .getSteps | Source code |
| .isCoefficientInEffect | Source code |
| .joinScpModelOutput | Source code |
| .levelsToContrastMatrix | Source code |
| .modelContrasts | Source code |
| .modelLevels | Source code |
| .modelSensitivity | Source code |
| .multiLevelsToContrastMatrix | Source code |
| .nipalsWrapper | Source code |
| .normalizeSCP | Source code |
| .pep2qvalue | Source code |
| .plotExplainedVarianceByFeature | Source code |
| .plotExplainedVarianceCombined | Source code |
| .plotPCA | Source code |
| .prettifyVariancePlot | Source code |
| .removeResponseVariables | Source code |
| .replaceDotVariable | Source code |
| .rowCV | Source code |
| .runAPCA | Source code |
| .runASCA | Source code |
| .runASCA.E | Source code |
| .sampledSensitivity | Source code |
| .scaleComponentsToUnity | Source code |
| .scpDifferentialAnalysisOnCoefficient | Source code |
| .scpDifferentialAnalysisOnContrast | Source code |
| .svdWrapper | Source code |
| .trimPlotLevels | Source code |
| .twoLevelsToContrastMatrix | Source code |
| ScpModel | Man page Source code |
| ScpModel-ComponentAnalysis | Man page |
| ScpModel-DataCorrection | Man page |
| ScpModel-DifferentialAnalysis | Man page |
| ScpModel-VarianceAnalysis | Man page |
| ScpModel-Workflow | Man page |
| ScpModel-class | Man page |
| ScpModelFit | Man page Source code |
| ScpModelFit-class | Man page |
| `scpModel<-` | Source code |
| `scpModelFilterThreshold<-` | Source code |
| `scpModelFitCoefficients<-` | Source code |
| `scpModelFitDf<-` | Source code |
| `scpModelFitEffects<-` | Source code |
| `scpModelFitLevels<-` | Source code |
| `scpModelFitList<-` | Source code |
| `scpModelFitResiduals<-` | Source code |
| `scpModelFitUvcov<-` | Source code |
| `scpModelFitVar<-` | Source code |
| `scpModelFormula<-` | Source code |
| `scpModelInputIndex<-` | Source code |
| addReducedDims | Man page Source code |
| aggregateFeaturesOverAssays | Man page Source code |
| class:ScpModel | Man page |
| class:ScpModelFit | Man page |
| computeSCR | Man page Source code |
| cumulativeSensitivityCurve | Man page Source code |
| divideByReference | Man page Source code |
| featureCV | Source code |
| jaccardIndex | Man page Source code |
| leduc_minimal | Man page |
| medianCVperCell | Man page Source code |
| mqScpData | Man page |
| normaliseSCP | Source code |
| normalizeSCP | Man page |
| pep2qvalue | Man page Source code |
| predictSensitivity | Man page Source code |
| readSCP | Man page Source code |
| readSCPfromDIANN | Man page Source code |
| readSingleCellExperiment | Man page Source code |
| reportMissingValues | Man page Source code |
| sampleAnnotation | Man page |
| scp1 | Man page |
| scpAnnotateResults | Man page Source code |
| scpComponentAggregate | Man page Source code |
| scpComponentAnalysis | Man page Source code |
| scpComponentBiplot | Man page Source code |
| scpComponentPlot | Man page Source code |
| scpDifferentialAggregate | Man page Source code |
| scpDifferentialAnalysis | Man page Source code |
| scpKeepEffect | Man page Source code |
| scpModel | Source code |
| scpModelCoefficients | Source code |
| scpModelComponentMethods | Man page |
| scpModelDf | Source code |
| scpModelEffectNames | Source code |
| scpModelEffects | Man page Source code |
| scpModelFeatureNames | Source code |
| scpModelFilterNPRatio | Man page Source code |
| scpModelFilterPlot | Man page Source code |
| scpModelFilterThreshold | Man page Source code |
| scpModelFilterThreshold<- | Man page |
| scpModelFitCoefficients | Source code |
| scpModelFitDf | Source code |
| scpModelFitEffects | Source code |
| scpModelFitElement | Source code |
| scpModelFitLevels | Source code |
| scpModelFitList | Source code |
| scpModelFitN | Source code |
| scpModelFitP | Source code |
| scpModelFitResiduals | Source code |
| scpModelFitUvcov | Source code |
| scpModelFitVar | Source code |
| scpModelFitVcov | Source code |
| scpModelFormula | Man page Source code |
| scpModelInput | Man page Source code |
| scpModelInputIndex | Source code |
| scpModelIntercept | Source code |
| scpModelN | Source code |
| scpModelNames | Man page Source code |
| scpModelP | Source code |
| scpModelResiduals | Man page Source code |
| scpModelUvcov | Source code |
| scpModelVar | Source code |
| scpModelVcov | Source code |
| scpModelWorkflow | Man page Source code |
| scpRemoveBatchEffect | Man page Source code |
| scpVarianceAggregate | Man page Source code |
| scpVarianceAnalysis | Man page Source code |
| scpVariancePlot | Man page Source code |
| scpVolcanoPlot | Man page Source code |
