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scp

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis


Bioconductor version: Release (3.18)

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 uclouvain.be>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scp")

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

Documentation

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

browseVignettes("scp")
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 processing and analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements
URL https://UCLouvain-CBIO.github.io/scp
Bug Reports https://github.com/UCLouvain-CBIO/scp/issues
See More
Suggests scpdata, testthat, knitr, BiocStyle, rmarkdown, ggplot2, patchwork, impute, scater, sva, preprocessCore, vsn, uwot
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me scpdata
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scp_1.12.0.tar.gz
Windows Binary scp_1.12.0.zip
macOS Binary (x86_64) scp_1.12.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scp
Bioc Package Browser https://code.bioconductor.org/browse/scp/
Package Short Url https://bioconductor.org/packages/scp/
Package Downloads Report Download Stats