scp
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Bioconductor version: 3.24 · Package version: 1.23.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
DOI: 10.18129/B9.bioc.scp
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scp")Details
| Maintainer | Christophe Vanderaa <vanderaa.christophe@gmail.com> |
| Author | Christophe Vanderaa [aut, cre] (ORCID: <https://orcid.org/0000-0001-7443-5427>), Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Léopold Guyot [ctb] |
| License | Artistic-2.0 |
| URL | https://UCLouvain-CBIO.github.io/scp |
| Bug Reports | https://github.com/UCLouvain-CBIO/scp/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellBasedAssays, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/scp/ |
Citation
From within R, enter citation("scp"):
Christophe Vanderaa, Laurent Gatto. scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis. doi:10.18129/B9.bioc.scp, R package version 1.23.0, https://bioconductor.org/packages/scp.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Advanced usage of scp
- Load Single-Cell Proteomics data using readSCP
- QFeatures in a nutshell
- Reporting missing values for Single Cell Proteomics
- Single Cell Proteomics data modelling using scplainer
- Single Cell Proteomics data processing and analysis
Download
Follow the installation instructions to use this package in your R session.
| Source package | scp_1.23.0.tar.gz |
| Windows binary (x86_64) | scp_1.23.0.zip |
| macOS binary (x86_64) | scp_1.23.0.tgz |
Dependencies
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
Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot
Reverse dependencies
Suggests Me (1): scpdata