# Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

## Documentation for package ‘scp’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addReducedDims | Add scplainer Component Analysis Results
aggregateFeaturesOverAssays | Aggregate features over multiple assays
class:ScpModel | Class to store the results of single-cell proteomics modelling
class:ScpModelFit | Class to store the components of an estimated model for a feature
computeSCR | Compute the sample over carrier ratio (SCR)
cumulativeSensitivityCurve | 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
predictSensitivity | Cumulative sensitivity curve
readSCP | Read single-cell proteomics tabular data
readSCPfromDIANN | Read single-cell proteomics tabular data
readSingleCellExperiment | Read single-cell proteomics tabular data
reportMissingValues | Four metrics to report missing values
sampleAnnotation | Single cell sample annotation
scp1 | Single Cell QFeatures data
scpAnnotateResults | Annotate single-cell proteomics analysis output
scpComponentAggregate | Component analysis for single cell proteomics
scpComponentAnalysis | Component analysis for single cell proteomics
scpComponentBiplot | Component analysis for single cell proteomics
scpComponentPlot | Component analysis for single cell proteomics
scpDifferentialAggregate | Differential abundance analysis for single-cell proteomics
scpDifferentialAnalysis | Differential abundance analysis for single-cell proteomics
scpKeepEffect | Correct single-cell proteomics data
ScpModel | Class to store the results of single-cell proteomics modelling
ScpModel-class | Class to store the results of single-cell proteomics modelling
ScpModel-ComponentAnalysis | Component analysis for single cell proteomics
ScpModel-DataCorrection | Correct single-cell proteomics data
ScpModel-DifferentialAnalysis | Differential abundance analysis for single-cell proteomics
ScpModel-VarianceAnalysis | Analysis of variance for single-cell proteomics
ScpModel-Workflow | Modelling single-cell proteomics data
scpModelComponentMethods | Component analysis for single cell proteomics
scpModelEffects | Class to store the results of single-cell proteomics modelling
scpModelFilterNPRatio | Class to store the results of single-cell proteomics modelling
scpModelFilterPlot | Modelling single-cell proteomics data
scpModelFilterThreshold | Class to store the results of single-cell proteomics modelling
scpModelFilterThreshold<- | Class to store the results of single-cell proteomics modelling
ScpModelFit | Class to store the components of an estimated model for a feature
ScpModelFit-class | Class to store the components of an estimated model for a feature
scpModelFormula | Class to store the results of single-cell proteomics modelling
scpModelInput | Class to store the results of single-cell proteomics modelling
scpModelNames | Class to store the results of single-cell proteomics modelling
scpModelResiduals | Class to store the results of single-cell proteomics modelling
scpModelWorkflow | Modelling single-cell proteomics data
scpRemoveBatchEffect | Correct single-cell proteomics data
scpVarianceAggregate | Analysis of variance for single-cell proteomics
scpVarianceAnalysis | Analysis of variance for single-cell proteomics
scpVariancePlot | Analysis of variance for single-cell proteomics
scpVolcanoPlot | Differential abundance analysis for single-cell proteomics