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Bioconductor - scp (development version)

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 (3.22)

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] ORCID: 0000-0001-7443-5427 , Laurent Gatto [aut] ORCID: 0000-0002-1520-2268 , Léopold Guyot [ctb]

Maintainer: Christophe Vanderaa <christophe.vanderaa at ugent.be>

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

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scp")
Details biocViews CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software Version 1.19.2 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License Artistic-2.0 Depends R (>= 4.3.0), QFeatures(>= 1.19.1) 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 See More 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.

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