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QFeatures

This is the development version of QFeatures; for the stable release version, see QFeatures.

Quantitative features for mass spectrometry data

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("QFeatures")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.11.1
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To
Suggests SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
System Requirements
Enhances
URL https://github.com/RforMassSpectrometry/QFeatures
Bug Reports https://github.com/RforMassSpectrometry/QFeatures/issues
See More
Depends On Me msqrob2, scp, scpdata
Imports Me MetaboAnnotation, MsExperiment, PSMatch
Suggests Me MsDataHub
Links To Me
Build Report  

Package Archives

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

Source Package QFeatures_1.11.1.tar.gz
Windows Binary QFeatures_1.11.1.zip
macOS Binary (x86_64) QFeatures_1.11.1.tgz
macOS Binary (arm64) QFeatures_1.11.1.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