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README.md
[![codecov.io](https://codecov.io/github/lgatto/MSnbase/coverage.svg?branch=master)](https://codecov.io/github/lgatto/MSnbase?branch=master) [![R-CMD-check-bioc](https://github.com/lgatto/MSnbase/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/lgatto/MSnbase/actions?query=workflow%3AR-CMD-check-bioc) # The `MSnbase` package <img align = "right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/MSnbase/MSnbase.png" height="200"> [**MSnbase**](https://lgatto.github.io/MSnbase/) is an R/Bioconductor package that provides infrastructure for plotting, manipulation and processing mass spectrometry and proteomics data. The project was started by [Laurent Gatto](https://lgatto.github.io/) in October 2010 (Mon Oct 4 23:35:23 2010, according to the git log) and has, since then, benefited from [various contributions](https://lgatto.github.io/msnbase-contribs/), in particular [Sebastian Gibb](https://sebastiangibb.de/) and [Johannes Rainer](https://github.com/jorainer). The official page is the Bioconductor landing page ([release](https://www.bioconductor.org/packages/release/bioc/html/MSnbase.html) or [devel](https://www.bioconductor.org/packages/devel/bioc/html/MSnbase.html) versions). The [github page](https://github.com/lgatto/MSnbase) page is for active development, issue tracking and forking/pulling purposes. To get an overview of the package, see the [*MSnbase-demo*](https://lgatto.github.io/MSnbase/articles/v01-MSnbase-demo.html) vignette. More vignettes are available in the *Articles* tab. ## Installation To install the package: ```r install.packages("BiocManager") BiocManager::install("MSnbase") ``` If you need the github version (not recommended unless you know what you are doing), use ```r BiocManager::install("lgatto/MSnbase") ``` ## Questions General questions should be asked on the [Bioconductor support forum](https://support.bioconductor.org/), using `MSnbase` to tag the question. Feel also free to open a GitHub [issue](https://github.com/lgatto/MSnbase/issues), in particular for bug reports. ## Citation To cite the `MSnbase` package in publications, please use: > Gatto L, Lilley KS. *`MSnbase` - an R/Bioconductor package for > isobaric tagged mass spectrometry data visualization, processing and > quantitation*. Bioinformatics. 2012 Jan > 15;28(2):288-9. doi:10.1093/bioinformatics/btr645. PubMed > [PMID:22113085](https://www.ncbi.nlm.nih.gov/pubmed/22113085). > *`MSnbase`, efficient and elegant R-based processing and > visualisation of raw mass spectrometry data*. Laurent Gatto, > Sebastian Gibb, Johannes Rainer. bioRxiv 2020.04.29.067868; doi: > https://doi.org/10.1101/2020.04.29.067868 ## Contributing Contributions to the package are more than welcome. If you want to contribute to this package, you should follow the same conventions as the rest of the functions. Please do get in touch (preferable opening a [github issue](https://github.com/lgatto/MSnbase/issues/)) to discuss any suggestions. The [`MSnbase` development vignette](https://lgatto.github.io/MSnbase/articles/v05-MSnbase-development.html) gives some background on the class infrastructure. Please note that this project is released with a [Contributor Code of Conduct](https://github.com/lgatto/MSnbase/blob/master/CONDUCT.md). By participating in this project you agree to abide by its terms.