# Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

## 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