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>

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

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")

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 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 1.8.0

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

Suggests testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, 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_1.8.0.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

Old Source Packages for BioC 3.16 Source Archive