DOI: 10.18129/B9.bioc.scp  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scp.

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: 3.17

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")):


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


biocViews CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version 1.10.1
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 4.2.0), QFeatures(>= 1.3.5)
Imports methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr
Suggests testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot
Depends On Me
Imports Me
Suggests Me scpdata
Links To Me
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