Package index • scp

All functions

scpModelComponentMethods scpComponentAnalysis() scpComponentAggregate() scpComponentPlot() scpComponentBiplot(): Component analysis for single cell proteomics
scpKeepEffect() scpRemoveBatchEffect(): Correct single-cell proteomics data
scpDifferentialAnalysis() scpDifferentialAggregate() scpVolcanoPlot(): Differential abundance analysis for single-cell proteomics
scpVarianceAnalysis() scpVarianceAggregate() scpVariancePlot(): Analysis of variance for single-cell proteomics
scpModelWorkflow() scpModelFilterPlot(): Modelling single-cell proteomics data
scpModelFormula() scpModelInput() scpModelFilterThreshold() scpModelFilterNPRatio() scpModelResiduals() scpModelEffects() scpModelNames() `scpModelFilterThreshold<-`(): Class to store the results of single-cell proteomics modelling
ScpModelFit ScpModelFit-class class:ScpModelFit: Class to store the components of an estimated model for a feature
addReducedDims(): Add scplainer Component Analysis Results
computeSCR(): Compute the sample over carrier ratio (SCR)
cumulativeSensitivityCurve() predictSensitivity(): Cumulative sensitivity curve
divideByReference(): Divide assay columns by a reference column
jaccardIndex(): Compute the pairwise Jaccard index
leduc_minimal: Minimally processed single-cell proteomics data set
medianCVperCell(): Compute the median coefficient of variation (CV) per cell
mqScpData: Example MaxQuant/SCoPE2 output
normalizeSCP(): Normalize single-cell proteomics (SCP) data
pep2qvalue(): Compute q-values
readSCP() readSCPfromDIANN() readSingleCellExperiment(): Read single-cell proteomics tabular data
reportMissingValues(): Four metrics to report missing values
sampleAnnotation: Single cell sample annotation
scp-defunct aggregateFeaturesOverAssays: Defunct Functions
scp1: Single Cell QFeatures data
scpAnnotateResults(): Annotate single-cell proteomics analysis output
scplainer: scplainer: linear models to understand mass spectrometry-based single-cell proteomics data