Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

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Documentation for package ‘scp’ version 1.12.0

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

Help Pages

aggregateFeaturesOverAssays	Aggregate features over multiple assays
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
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 data as a QFeatures object from tabular data and metadata
readSCPfromDIANN	Read DIA-NN output as a QFeatures objects for single-cell proteomics data
readSingleCellExperiment	Read SingleCellExperiment from tabular data
reportMissingValues	Four metrics to report missing values
sampleAnnotation	Single cell sample annotation
scp1	Single Cell QFeatures data