https://github.com/fgcz/rawrr

Access Orbitrap data in R lang using C# mono assembly - bioconductor package
https://github.com/fgcz/rawrr

fast mass-spectrometry multiplatform orbitrap-ms rpackage

Last synced: 7 days ago
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Access Orbitrap data in R lang using C# mono assembly - bioconductor package

• Host: GitHub
• URL: https://github.com/fgcz/rawrr
• Owner: fgcz
• Created: 2020-08-25T08:37:00.000Z (over 4 years ago)
• Default Branch: devel
• Last Pushed: 2024-12-04T14:27:35.000Z (18 days ago)
• Last Synced: 2024-12-04T15:29:50.910Z (18 days ago)
• Topics: fast, mass-spectrometry, multiplatform, orbitrap-ms, rpackage
• Language: R
• Homepage: https://bioconductor.org/packages/rawrr/
• Size: 3.15 MB
• Stars: 54
• Watchers: 8
• Forks: 9
• Open Issues: 12
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-proteomics - rawrr - R - A great package that can read in raw thermo files! Thats great to me, because I always find it tedious to convert a raw file into a mzML or mzXML file - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00866) (5. Raw Data Analysis / Table of Contents)

README

        
[![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)

[![JPR](https://img.shields.io/badge/JPR-10.1021%2Facs.jproteome.0c00866-brightgreen)](http://dx.doi.org/10.1021/acs.jproteome.0c00866)

[![codecov](https://codecov.io/gh/fgcz/rawrr/branch/master/graph/badge.svg?token=OO4Y7G4UUX)](https://codecov.io/gh/fgcz/rawrr)

[![bioc-check](https://bioconductor.org/shields/build/devel/bioc/rawrr.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/rawrr/)

![Downloads](https://img.shields.io/github/downloads/fgcz/rawrr/total)

![rawrrHexSticker](rawrr_logo.png)

# rawrr

The package provides access to proprietary Thermo Fisher Scientific Orbitrap instrument data as a stand-alone R package or serves as [MsRawFileReaderBackend](https://github.com/cpanse/MsBackendRawFileReader) for the Bioconductor [Spectra](https://bioconductor.org/packages/Spectra/) package.

rawrr wraps the functionality of the [RawFileReader](https://github.com/thermofisherlsms/RawFileReader) [.NET assembly](https://www.mono-project.com/docs/advanced/assemblies-and-the-gac/). 

Test files are provided by the [tartare](https://bioconductor.org/packages/tartare/) ExperimentData package.

## Install

Please follow the [INSTALL](https://bioconductor.org/packages/release/bioc/install/rawrr/INSTALL) instructions provided through 

https://bioconductor.org/packages/rawrr/

The latest source package build [bioconductor devel branch](https://bioconductor.org/packages/devel/bioc/html/rawrr.html) can be found through

https://fgcz-ms.uzh.ch/~cpanse/rawrr/

## Manuscript

http://dx.doi.org/10.1021/acs.jproteome.0c00866

## Talks

- [rawrr - invoking managed code using ThermoFisher.CommonCore.RawFileReader;](http://fgcz-ms.uzh.ch/~cpanse/talks/20211123-rawrrRcpp_MetaRbolimics2021.html) presentaton at 

[3rd de.NBI / ELIXIR-DE metaRbolomics Hackathon 2021](https://www.denbi.de/news/1299-3rd-de-nbi-elixir-de-metarbolomics-hackathon) in Lutherstadt Wittenberg (22-24 November); [code snippets](https://github.com/cpanse/rawrrRcpp).

- [MsRawFileReaderBackend](https://bioconductor.org/packages/MsBackendRawFileReader/) presentaton at

[European Biocondutor Meeting, de Duve Institute, UCLouvain, Campus de Woluw ́e Brussels, Belgium, Dec 2019](http://fgcz-ms.uzh.ch/~cpanse/talks/rawR_EuroBioc2019_Brussels_88c9.pdf)