QFeatures
Quantitative features for mass spectrometry data
Bioconductor version: 3.24 · Package version: 1.23.2
The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("QFeatures")Details
| Maintainer | Laurent Gatto <laurent.gatto@uclouvain.be> |
| Author | Laurent Gatto [aut, cre] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Christophe Vanderaa [aut] (ORCID: <https://orcid.org/0000-0001-7443-5427>), Karolína Kryštofová [ctb] (ORCID: <https://orcid.org/0009-0004-2896-2188>), Léopold Guyot [ctb] (ORCID: <https://orcid.org/0009-0005-2217-3855>) |
| License | Artistic-2.0 |
| URL | https://rformassspectrometry.github.io/QFeatures |
| Bug Reports | https://github.com/rformassspectrometry/QFeatures/issues |
| Downloads rank | 4177 |
| Source branch | devel |
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
Documentation
- Data visualization from a QFeatures object
- Imputing quantitative proteomics data
- Load mass spectrometry-based proteomics data using readQFeatures()
- Processing quantitative proteomics data with QFeatures
- Quantitative features for mass spectrometry data
- Supported input formats for readQFeatures()
Download
Follow the installation instructions to use this package in your R session.
| Source package | QFeatures_1.23.2.tar.gz |
| Windows binary (x86_64) | QFeatures_1.23.2.zip |
| macOS binary (arm64) | QFeatures_1.23.2.tgz |
| macOS binary (x86_64) | QFeatures_1.23.2.tgz |
Dependencies
Depends: R (>= 4.1), MultiAssayExperiment (>= 1.33.6)
Imports: methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics (>= 0.53.4), ProtGenerics (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.25.3), igraph, grDevices, plotly, tidyr, dplyr, tidyselect, reshape2
Suggests: SingleCellExperiment, MsDataHub (>= 1.11.5), arrow, Matrix, HDF5Array, ggplot2, gplots, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
Reverse dependencies
Depends On Me (4): hdxmsqc, msqrob2, scp, scpdata
Imports Me (9): DaparToolshed, DaparToolshedData, MetaboAnnotation, MsExperiment, mspms, omicsGMF, proBatch, PSMatch, QFeaturesGUI
Suggests Me (2): MsDataHub, RforProteomics