QFeatures

DOI: 10.18129/B9.bioc.QFeatures    

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

Quantitative features for mass spectrometry data

Bioconductor version: Development (3.17)

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")

 

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 1.9.2
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, 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_1.9.2.tar.gz
Windows Binary QFeatures_1.9.2.zip
macOS Binary (x86_64) QFeatures_1.9.2.tgz
macOS Binary (arm64) QFeatures_1.9.2.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: