QFeatures

DOI: 10.18129/B9.bioc.QFeatures    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see QFeatures.

Quantitative features for mass spectrometry data

Bioconductor version: 3.15

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	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	Artistic-2.0
Depends	R (>= 4.0), MultiAssayExperiment
Imports	methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics(>= 1.19.3), AnnotationFilter, lazyeval, Biobase, MsCoreUtils(>= 1.1.2), igraph, plotly
LinkingTo
Suggests	SingleCellExperiment, 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, PSMatch
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	QFeatures_1.6.0.tar.gz
Windows Binary	QFeatures_1.6.0.zip
macOS Binary (x86_64)	QFeatures_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QFeatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QFeatures
Package Short Url	https://bioconductor.org/packages/QFeatures/
Package Downloads Report	Download Stats