scp

DOI: 10.18129/B9.bioc.scp    

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: Release (3.15)

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics (SCP) data. The package is an extension to the 'QFeatures' package designed for SCP applications.

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	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	Artistic-2.0
Depends	R (>= 4.0), QFeatures(>= 1.3.5)
Imports	methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr, rlang
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_1.6.0.tar.gz
Windows Binary	scp_1.6.0.zip
macOS Binary (x86_64)	scp_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scp
Package Short Url	https://bioconductor.org/packages/scp/
Package Downloads Report	Download Stats