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README.md
## Quantitative features for mass spectrometry data [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R-CMD-check-bioc](https://github.com/RforMassSpectrometry/QFeatures/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/RforMassSpectrometry/QFeatures/actions?query=workflow%3AR-CMD-check-bioc) [![codecov.io](https://codecov.io/github/rformassspectrometry/QFeatures/coverage.svg?branch=master)](https://codecov.io/github/rformassspectrometry/QFeatures?branch=master) [![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0) <img src="https://raw.githubusercontent.com/rformassspectrometry/stickers/master/QFeatures/QFeatures.png" height="150"> ### What is QFeatures? `QFeatures` is a [Bioconductor package](http://bioconductor.org/packages/QFeatures) that provides infrastructure to management and process quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manage quantitative data across different assay levels (such as precursors, peptide spectrum matches, peptides and proteins or protein groups) in a coherent and tractable format. If you are familiar with the `MSnbase` package, `QFeatures` could be summarised with: > Evolving `MSnSet` data towards `SummarizedExperiment`, but for MS > data. ### Getting started The `QFeatures` class is used to manage and process quantitative features for high-throughput mass spectrometry assays. See the [QFeatures introduction](https://rformassspectrometry.github.io/QFeatures/articles/QFeatures.html) to get started and the [Processing quantitative proteomics data with QFeatures](https://rformassspectrometry.github.io/QFeatures/articles/Processing.html) vignette for a real-life application. Visualisation of quantitative mass spectrometry data contained in a `QFeatures` object is illustrated in the [Data visualisation](https://rformassspectrometry.github.io/QFeatures/articles/Visualization.html) vignette. ### License The `QFeatures` code is provided under a permissive [Artistic 2.0 license](https://opensource.org/licenses/Artistic-2.0). The documentation, including the manual pages and the vignettes, are distributed under a [CC BY-SA license](https://creativecommons.org/licenses/by-sa/4.0/).