scp

DOI: 10.18129/B9.bioc.scp  

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Bioconductor version: Release (3.17)

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 "4.3") 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 1.10.1
In Bioconductor since BioC 3.12 (R-4.0) (3 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_1.10.1.tar.gz
Windows Binary scp_1.10.1.zip
macOS Binary (x86_64) scp_1.10.1.tgz
macOS Binary (arm64) scp_1.9.0.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 3.17 Source Archive

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