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README.md
# Managing mass spectrometry experiments [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![R-CMD-check-bioc](https://github.com/RforMassSpectrometry/MsExperiment/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/RforMassSpectrometry/MsExperiment/actions?query=workflow%3AR-CMD-check-bioc) [![codecov](https://codecov.io/gh/rformassspectrometry/MsExperiment/branch/main/graph/badge.svg?token=IEBQZJAJVI)](https://codecov.io/gh/rformassspectrometry/MsExperiment) [![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0) [![years in bioc](http://bioconductor.org/shields/years-in-bioc/MsExperiment.svg)](https://bioconductor.org/packages/release/bioc/html/MsExperiment.html) [![Ranking by downloads](http://bioconductor.org/shields/downloads/release/MsExperiment.svg)](https://bioconductor.org/packages/stats/bioc/MsExperiment/) [![build release](http://bioconductor.org/shields/build/release/bioc/MsExperiment.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/MsExperiment/) [![build devel](http://bioconductor.org/shields/build/devel/bioc/MsExperiment.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/MsExperiment/) The `MsExperiment` package provides the `MsExperiment` class that can be used to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry experiment. This includes - experimental design - data files - raw data: spectra and chromatograms - proteomics identification results and protein database - quantitative features The respective data handling functionality is handled by dedicated packages such as `Spectra` for spectra data, `QFeatures` for quantitative features, `Biostrings` for fasta files, ... See the package [homepage](https://rformassspectrometry.github.io/MsExperiment) for more information. This package is part of the RforMassSpectrometry initiative: https://www.rformassspectrometry.org/ # Installation The package can be installed with ```r install.packages("BiocManager") BiocManager::install("MsExperiment") ``` # Contributions Contributions are highly welcome and should follow the [contribution guidelines](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions). Also, please check the coding style guidelines in the [RforMassSpectrometry vignette](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html).