QFeatures

DOI: 10.18129/B9.bioc.QFeatures  

Quantitative features for mass spectrometry data

Bioconductor version: Release (3.16)

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.

Author: Laurent Gatto [aut, cre] , Christophe Vanderaa [aut]

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QFeatures")

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("QFeatures")

 

HTML	R Script	Data visualization from a QFeatures object
HTML	R Script	Processing quantitative proteomics data with QFeatures
HTML	R Script	Quantitative features for mass spectrometry data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), MultiAssayExperiment
Imports	methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics(>= 1.27.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils(>= 1.7.2), igraph, plotly
LinkingTo
Suggests	SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, magrittr, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
SystemRequirements
Enhances
URL	https://github.com/RforMassSpectrometry/QFeatures
BugReports	https://github.com/RforMassSpectrometry/QFeatures/issues
Depends On Me	msqrob2, scp, scpdata
Imports Me	MetaboAnnotation, MsExperiment, PSMatch
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	QFeatures_1.8.0.tar.gz
Windows Binary	QFeatures_1.8.0.zip
macOS Binary (x86_64)	QFeatures_1.8.0.tgz
macOS Binary (arm64)	QFeatures_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QFeatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QFeatures
Bioc Package Browser	https://code.bioconductor.org/browse/QFeatures/
Package Short Url	https://bioconductor.org/packages/QFeatures/
Package Downloads Report	Download Stats