scp

DOI: 10.18129/B9.bioc.scp  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scp.

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 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
LinkingTo
Suggests	testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot
SystemRequirements
Enhances
URL	https://UCLouvain-CBIO.github.io/scp
BugReports	https://github.com/UCLouvain-CBIO/scp/issues
Depends On Me
Imports Me
Suggests Me	scpdata
Links To Me
Build Report

Package Archives

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

Source Package	scp_1.8.0.tar.gz
Windows Binary	scp_1.8.0.zip
macOS Binary (x86_64)	scp_1.8.0.tgz
macOS Binary (arm64)	scp_1.8.0.tgz
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