QFeatures

This is the released version of QFeatures; for the devel version, see QFeatures.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Quantitative features for mass spectrometry data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1520-2268 , Christophe Vanderaa [aut] ORCID: 0000-0001-7443-5427 , Karolína Kryštofová [ctb] ORCID: 0009-0004-2896-2188 , Léopold Guyot [ctb]

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

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

Laurent Gatto, Christophe Vanderaa. QFeatures: Quantitative features for mass spectrometry data. doi:10.18129/B9.bioc.QFeatures, R package version 1.22.0, https://bioconductor.org/packages/QFeatures.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.22.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	Artistic-2.0
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 (>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2
System Requirements
URL	https://rformassspectrometry.github.io/QFeatures
Bug Reports	https://github.com/rformassspectrometry/QFeatures/issues

Suggests	SingleCellExperiment, MsDataHub (>= 1.11.5), arrow, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
Linking To
Enhances
Depends On Me	hdxmsqc, msqrob2, scp, scpdata
Imports Me	MetaboAnnotation, MsExperiment, mspms, omicsGMF, proBatch, PSMatch
Suggests Me	MsDataHub
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	QFeatures_1.22.0.tar.gz
Windows Binary (x86_64)	QFeatures_1.22.0.zip
macOS Binary (big-sur-x86_64)	QFeatures_1.22.0.tgz
macOS Binary (sonoma-arm64)	QFeatures_1.22.0.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