https://github.com/jorainer/metaboannotationtutorials
Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages
https://github.com/jorainer/metaboannotationtutorials
annotation mass-spectrometry metabolomics
Last synced: 4 months ago
JSON representation
Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages
- Host: GitHub
- URL: https://github.com/jorainer/metaboannotationtutorials
- Owner: jorainer
- Created: 2022-01-21T14:57:34.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-12-05T09:04:16.000Z (almost 2 years ago)
- Last Synced: 2025-01-20T22:55:06.992Z (9 months ago)
- Topics: annotation, mass-spectrometry, metabolomics
- Language: TeX
- Homepage: https://jorainer.github.io/MetaboAnnotationTutorials/
- Size: 14 MB
- Stars: 7
- Watchers: 3
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
Awesome Lists containing this project
README
# Use Cases and Examples for Annotation of Untargeted Metabolomics Data
[](https://creativecommons.org/licenses/by-nc/4.0/)
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 packages. Refer to the original article [A Modular and
Expandable Ecosystem for Metabolomics Data Annotation in
R](https://doi.org/10.3390/metabo12020173) to **cite** this package/repository
or any functionality described here.
## Installation
Requirements: R version >= 4.2 (and hence Bioconductor 3.15) is needed.
The R packages as well as the example files used in this document can be
installed with the R code below:
```r
install.packages("BiocManager")
BiocManager::install("jorainer/MetaboAnnotationTutorials",
dependencies = TRUE, ask = FALSE, update = TRUE)
```
Alternatively, the packages can be installed individually with:
```r
install.packages("BiocManager")
BiocManager::install("ProtGenerics")
## Packages with low-level core functionality
BiocManager::install("MsCoreUtils")
BiocManager::install("MetaboCoreUtils")
## Packages with high-level user functionality
BiocManager::install("Spectra")
BiocManager::install("MetaboAnnotation")
BiocManager::install("CompoundDb")
## Support for MGF files
BiocManager::install("MsBackendMgf")
## Support for MassBank
BiocManager::install("MsBackendMassbank")
## Support for MSP files
BiocManager::install("MsBackendMsp")
```
The source code for this document along with the test data can be downloaded
from the github repository https://github.com/jorainer/MetaboAnnotationTutorials
with the command (or alternatively downloading the zip archive directly from the
github page).
```
git clone https://github.com/jorainer/MetaboAnnotationTutorials
```
## Contribution
For contributions, see the [RforMassSpectrometry contributions
guideline](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions).
## Code of Conduct
See the [RforMassSpectrometry Code of
Conduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#code-of-conduct).
## Additional documentation resources and tutorials
- Tutorial with additional examples and explanations for MS2-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/