https://github.com/jorainer/spectra_workshop
Workshop about the RforMassSpectrometry Spectra R package.
https://github.com/jorainer/spectra_workshop
Last synced: 3 months ago
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Workshop about the RforMassSpectrometry Spectra R package.
- Host: GitHub
- URL: https://github.com/jorainer/spectra_workshop
- Owner: jorainer
- Created: 2020-01-10T07:07:41.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-01-20T11:58:10.000Z (over 5 years ago)
- Last Synced: 2025-01-20T22:55:00.485Z (5 months ago)
- Language: HTML
- Size: 43.9 MB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# RforMassSpectrometry/Spectra workshop
*Presenter*: Johannes Rainer, Institute for Biomedicine, Eurac Research,
Bolzano, Italy.
This repository contains all files and data for my part of the [metaRbolomics
hackathon plus](https://rfmf-mpf-2020.sciencesconf.org/resource/page/id/32)
workshop of the [European RFMF Metabomeeting
2020](https://rfmf-mpf-2020.sciencesconf.org/) in Toulouse.
The workshop provides background information on the new mass spectrometry
infrastructure which is being developed as part of the
[RforMassSpectrometry](https://www.rformassspectrometry.org) initiative and
shows its usage on the example of matching an experimental MS2 spectrum against
a MS2 library. We will thus in particular focus on the functionality of the
[Spectra](https://github.com/RforMassSpectrometry/Spectra) R package.
The workshop consists of two parts:
- static presentation:
[spectra_workshop_static.Rmd](spectra_workshop_static.Rmd), [html
view](https://jorainer.github.io/spectra_workshop/spectra_workshop_static.html).
- interactive presentation:
[spectra_workshop_interactive.org](spectra_workshop_interactive.org) (Emacs
org-mode file); *Rmd* version:
[spectra_workshop_interactive.Rmd](spectra_workshop_interactive.Rmd).
## Main topics
- What is [RforMassSpectrometry](https://www.rformassspectrometry.org/)?
- What is available as of now? (`MsCoreUtils`, `Spectra`)
- Flexible infrastructure: use different backends to load, represent, store
data.
- Use case: match measured MS2 spectrum against database.
- Missing pieces:
- plotting functionality
- backends to import/work with MGF data, MassBank, ...
- other things we haven't thought of?
- How can **you** contribute?
## Installation instructions
To run the examples above a recent version of R is required (>= 3.6.1) and a set
of packages, which can be installed with the commands below.
```r
install.packages("BiocManager")
BiocManager::install(c("remotes", "magrittr", "rmarkdown"))
BiocManager::install("RforMassSpectrometry/Spectra")
BiocManager::install("RforMassSpectrometry/MsBackendHmdb")
BiocManager::install(c("mzR", "BiocStyle"))
```
and use `git clone https://github.com/jorainer/spectra_workshop` to clone the
repository to your computer.
Note: on Windows you might have to use `type = "source"` in the installation
calls above to force installation of packages from source instead of using the
pre-built packages.