scp
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see scp.
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Bioconductor version: 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("scp")):
Installation
To install this package, start R (version "4.4") 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 |
| Reporting missing values | HTML | R Script |
| Single Cell Proteomics data modelling | HTML | R Script |
| Single Cell Proteomics data processing and analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 |
See More
| 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 | scp_1.14.0.tar.gz |
| Windows Binary (x86_64) | scp_1.14.0.zip |
| macOS Binary (x86_64) | scp_1.14.0.tgz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scp/ |
| Package Short Url | https://bioconductor.org/packages/scp/ |
| Package Downloads Report | Download Stats |