https://github.com/jorainer/annotation_ecosystem
Supplementary material for the annotation ecosystem paper.
https://github.com/jorainer/annotation_ecosystem
Last synced: 3 months ago
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Supplementary material for the annotation ecosystem paper.
- Host: GitHub
- URL: https://github.com/jorainer/annotation_ecosystem
- Owner: jorainer
- Created: 2021-12-14T07:38:59.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-01-28T08:31:35.000Z (over 3 years ago)
- Last Synced: 2025-01-20T22:54:55.651Z (5 months ago)
- Language: TeX
- Size: 5.21 MB
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
**This repository is deprecated, please use
[jorainer/MetaboAnnotationTutorials](https://github.com/jorainer/MetaboAnnotationTutorials)
instead**
# Use cases and examples for annotation of non-target metabolomics data
This repository provides use cases and examples for the annotation of non-target
metabolomics or small compound MS data using the `MetaboAnnotation` and
`MetaboCoreUtils` R packges.
## Installation
The R packages used in this examples can be installed with the R code below:
```
install.packages("BiocManager")
BiocManager::install(c("xcms", "pander"))
BiocManager::install(c("Spectra", "MsCoreUtils", "MetaboCoreUtils"))
BiocManager::install("RforMassSpectrometry/CompoundDb")
BiocManager::install("RforMassSpectrometry/MetaboAnnotation")
```
The source code for this document along with the test data can be downloaded
from the github repository https://github.com/jorainer/annotation_ecosystem with
the command (or alternatively downloading the zip archive directly from the
github page; note that [git-lfs](https://git-lfs.github.com/) needs to be
installed for the command below to work).
```
git clone https://github.com/jorainer/annotation_ecosystem
```
## Additional documentation resources and tutorials
- Tutorial with additional examples and explanations for $MS^2$-based
annotations: https://jorainer.github.io/SpectraTutorials/
- Repository of the `MsCoreUtils` package:
https://rformassspectrometry.github.io/MsCoreUtils/
- Repository of the `MetaboCoreUtils` package:
https://rformassspectrometry.github.io/MetaboCoreUtils/
- Repository of the `Spectra` package:
https://rformassspectrometry.github.io/Spectra/
- Repository of the `MetaboAnnotation` package:
https://rformassspectrometry.github.io/MetaboAnnotation/
- Repository of the `CompoundDb` package:
https://rformassspectrometry.github.io/CompoundDb/