Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

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Documentation for package ‘scp’ version 1.18.0

• 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
aggregateFeaturesOverAssays-deprecated	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