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Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: Release (3.19)

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Author: Christophe Vanderaa [aut, cre] , Laurent Gatto [aut]

Maintainer: Christophe Vanderaa <christophe.vanderaa at>

Citation (from within R, enter citation("scp")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Advanced usage of `scp` HTML R Script
Load data using readSCP HTML R Script
QFeatures in a nutshell HTML R Script
Reporting missing values HTML R Script
Single Cell Proteomics data modelling HTML R Script
Single Cell Proteomics data processing and analysis HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.3.0), QFeatures(>= 1.13.5)
Imports dplyr, IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils
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Suggests BiocStyle, MsDataHub(>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vsn, uwot
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Source Package scp_1.14.0.tar.gz
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