scp

This is the development version of scp; for the stable release version, see scp.

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scp")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software
Version	1.13.4
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	Artistic-2.0
Depends	R (>= 4.3.0), QFeatures(>= 1.13.5)
Imports	dplyr, 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, MsDataHub(>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, 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
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/scp/
Package Downloads Report	Download Stats