This repository has moved to Codeberg. This mirror is no longer maintained.
This package provides spectral libraries in R.
For now, the version of MassBank used and the Zenodo repository IDs are added manually to the file names. This might change in the future.
Also look at https://github.com/taxonomicallyinformedannotation/tima-isdb-pos and https://github.com/taxonomicallyinformedannotation/tima-isdb-neg
General: https://doi.org/10.1038/nbt.3597 Repository used:https://doi.org/10.5281/zenodo.11566051
- The RforMassSpectrometry packages suite: https://doi.org/10.3390/metabo12020173
- MassBank: https://doi.org/10.5281/zenodo.3378723
- Merlin: https://doi.org/10.5281/zenodo.13911806
| Package | Version | Citation |
|---|---|---|
| base | 4.5.1 | R Core Team (2025) |
| BiocManager | 1.30.26 | Morgan and Ramos (2025) |
| BiocVersion | 3.22.0 | Morgan (2025) |
| knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) |
| logger | 0.4.1 | Daróczi and Wickham (2025) |
| rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) |
| tidyverse | 2.0.0 | Wickham et al. (2019) |
| tima | 2.12.0 | Rutz et al. (2019); Rutz and Allard (2025) |
| yaml | 2.3.10 | Garbett et al. (2024) |
Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown.
Daróczi, Gergely, and Hadley Wickham. 2025. logger: A Lightweight, Modern and Flexible Logging Utility. https://doi.org/10.32614/CRAN.package.logger.
Garbett, Shawn P, Jeremy Stephens, Kirill Simonov, Yihui Xie, Zhuoer Dong, Hadley Wickham, Jeffrey Horner, et al. 2024. yaml: Methods to Convert r Data to YAML and Back. https://doi.org/10.32614/CRAN.package.yaml.
Morgan, Martin. 2025. BiocVersion: Set the Appropriate Version of Bioconductor Packages. https://doi.org/10.18129/B9.bioc.BiocVersion.
Morgan, Martin, and Marcel Ramos. 2025. BiocManager: Access the Bioconductor Project Package Repository. https://doi.org/10.32614/CRAN.package.BiocManager.
R Core Team. 2025. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Rutz, Adriano, and Pierre-Marie Allard. 2025. tima: Taxonomically Informed Metabolite Annotation. https://doi.org/10.5281/zenodo.5797920.
Rutz, Adriano, Miwa Dounoue-Kubo, Simon Ollivier, Jonathan Bisson, Mohsen Bagheri, Tongchai Saesong, Samad Nejad Ebrahimi, Kornkanok Ingkaninan, Jean-Luc Wolfender, and Pierre-Marie Allard. 2019. “Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation.” Frontiers in Plant Science 10. https://doi.org/10.3389/FPLS.2019.01329.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.
Xie, Yihui. 2014. “knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
———. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.
———. 2025. knitr: A General-Purpose Package for Dynamic Report Generation in R. https://yihui.org/knitr/.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.
