scp

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: Release (3.20)

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 ugent.be>

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

Installation

To install this package, start R (version "4.4") 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 modelling	HTML	R Script
Single Cell Proteomics data processing and analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version	1.16.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	Artistic-2.0
Depends	R (>= 4.3.0), QFeatures(>= 1.13.5)
Imports	IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils
System Requirements
URL	https://UCLouvain-CBIO.github.io/scp
Bug Reports	https://github.com/UCLouvain-CBIO/scp/issues

Suggests	BiocStyle, BiocGenerics, MsDataHub(>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, 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_1.16.0.tar.gz
Windows Binary (x86_64)	scp_1.16.0.zip
macOS Binary (x86_64)	scp_1.16.0.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