https://github.com/lgatto/2020-msnbase-v2
MSnbase v2 paper
https://github.com/lgatto/2020-msnbase-v2
bioconductor mass-spectrometry massspectrometry metabolomics msnbase proteomics
Last synced: about 2 months ago
JSON representation
MSnbase v2 paper
- Host: GitHub
- URL: https://github.com/lgatto/2020-msnbase-v2
- Owner: lgatto
- Created: 2019-04-13T08:09:33.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2020-12-02T20:37:27.000Z (over 4 years ago)
- Last Synced: 2025-01-20T22:55:23.098Z (3 months ago)
- Topics: bioconductor, mass-spectrometry, massspectrometry, metabolomics, msnbase, proteomics
- Language: TeX
- Homepage: https://lgatto.github.io/2020-msnbase-v2/
- Size: 9.89 MB
- Stars: 1
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data
We present version 2 of the **MSnbase** R/Bioconductor
package. **MSnbase** provides infrastructure for the manipulation,
processing and visualisation of mass spectrometry data. We focus on
the new *on-disk* infrastructure, that allows the handling of large
raw mass spectrometry experiments on commodity hardware and illustrate
how the package is used for elegant data processing, method
development and visualisation.
- The [manuscript](https://github.com/lgatto/2020-msnbase-v2/raw/master/msnbase2.pdf).
- [Supplementary material](https://github.com/lgatto/2020-msnbase-v2/raw/master/large_experiment_processing.pdf) presenting a large scale analysis with the on-disk backend.
- Presentation of the software at ISMB 2020: [https://youtu.be/lSiVZnrV5Bc](https://youtu.be/lSiVZnrV5Bc).
The code to reproduce the analyses and figures:
- [S01-ondisk.R](https://github.com/lgatto/2020-msnbase-v2/blob/master/S01-ondisk.R)
- [S02-boxcar.R](https://github.com/lgatto/2020-msnbase-v2/blob/master/S02-boxcar.R)
- [S03-vis.R](https://github.com/lgatto/2020-msnbase-v2/blob/master/S03-vis.R)
More information:
- The [MSnbase website](http://lgatto.github.io/MSnbase/)
- MSnbase's [Bioconductor landing page](http://bioconductor.org/packages/release/bioc/html/MSnbase.html)
Citation:
> 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
Now published in Journal of Proteome Research doi: [10.1021/acs.jproteome.0c00313](http://dx.doi.org/10.1021/acs.jproteome.0c00313)