QFeatures

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see QFeatures.

Quantitative features for mass spectrometry data

Bioconductor version: 3.14

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 "4.1") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software

Version 1.4.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 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

System Requirements

URL https://github.com/RforMassSpectrometry/QFeatures

Bug Reports https://github.com/RforMassSpectrometry/QFeatures/issues

Suggests SingleCellExperiment, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, magrittr, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap

Linking To

Enhances

Depends On Me msqrob2, scp, scpdata

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package QFeatures_1.4.0.tar.gz

Windows Binary QFeatures_1.4.0.zip

macOS 10.13 (High Sierra) QFeatures_1.4.0.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

Old Source Packages for BioC 3.14 Source Archive