SAPID

Lifecycle: experimental R-CMD-check Codecov test coverage r-universe badge DOI

A Strategy to Analyze Plant Extracts Taste In Depth.

⚠️ This repository is not maintained and will not be except for extreme interest. It has just been opened for the sake of transparency.

Installation

As the package is not (yet) available on CRAN, you will need to install with:

install.packages(
  "sapid",
  repos = c(
    "https://adafede.r-universe.dev",
    "https://bioc.r-universe.dev",
    "https://cloud.r-project.org"
  )
)

Main Citations

SAPID

Article: https://doi.org/10.1016/j.crfs.2025.101043

According to which steps you used, please give credit to the authors of the tools/resources used.

mzmine

General: https://doi.org/10.1038/s41587-023-01690-2

SIRIUS

General: https://doi.org/10.1038/s41592-019-0344-8

LOTUS

General: https://doi.org/10.7554/eLife.70780

⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5794106

ISDB

General: https://doi.org/10.1021/acs.analchem.5b04804

⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5607185

TIMA

General: https://doi.org/10.3389/fpls.2019.01329

⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5797920

Others

Additional software credits

Package Version Citation
AlpsNMR 4.10.0 Madrid-Gambin et al. (2020)
base 4.5.1 R Core Team (2025)
BiocManager 1.30.26 Morgan and Ramos (2025)
BiocVersion 3.21.1 Morgan (2024)
BSDA 1.2.2 Arnholt and Evans (2023)
cascade 0.0.0.9001 Rutz and Wolfender (2023); Rutz (2025)
dendextend 1.19.1 Galili (2015)
FactoMineR 2.12 Lê, Josse, and Husson (2008)
ggbump 0.1.0 Sjoberg (2020)
ggpubr 0.6.1 Kassambara (2025)
ggraph 2.2.2 Pedersen (2025)
ggrepel 0.9.6 Slowikowski (2024)
igraph 2.1.4 Csardi and Nepusz (2006); Csárdi et al. (2025)
khroma 1.16.0 Frerebeau (2025)
knitr 1.50 Xie (2014); Xie (2015); Xie (2025)
NMRphasing 1.0.7 Jiang (2025)
pkgload 1.4.0 Wickham et al. (2024)
rmarkdown 2.29 Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024)
scales 1.4.0 Wickham, Pedersen, and Seidel (2025)
SensoMineR 1.28 Husson, Le, and Cadoret (2025)
stringi 1.8.7 Gagolewski (2022)
testthat 3.2.3 Wickham (2011)
tidytable 0.11.2 Fairbanks (2024)
tidyverse 2.0.0 Wickham et al. (2019)
treemapify 2.5.6 Wilkins (2023)

References

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.
Arnholt, Alan T., and Ben Evans. 2023. BSDA: Basic Statistics and Data Analysis. https://github.com/alanarnholt/BSDA.
Csardi, Gabor, and Tamas Nepusz. 2006. “The Igraph Software Package for Complex Network Research.” InterJournal Complex Systems: 1695. https://igraph.org.
Csárdi, Gábor, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, and Kirill Müller. 2025. igraph: Network Analysis and Visualization in r. https://doi.org/10.5281/zenodo.7682609.
Fairbanks, Mark. 2024. tidytable: Tidy Interface to “data.table”. https://markfairbanks.github.io/tidytable/.
Frerebeau, Nicolas. 2025. khroma: Colour Schemes for Scientific Data Visualization. Pessac, France: Université Bordeaux Montaigne. https://doi.org/10.5281/zenodo.1472077.
Gagolewski, Marek. 2022. “stringi: Fast and Portable Character String Processing in R.” Journal of Statistical Software 103 (2): 1–59. https://doi.org/10.18637/jss.v103.i02.
Galili, Tal. 2015. “dendextend: An r Package for Visualizing, Adjusting, and Comparing Trees of Hierarchical Clustering.” Bioinformatics. https://doi.org/10.1093/bioinformatics/btv428.
Husson, Francois, Sebastien Le, and Marine Cadoret. 2025. SensoMineR: Sensory Data Analysis. http://sensominer.free.fr.
Jiang, Aixiang. 2025. NMRphasing: Phase Error Correction and Baseline Correction for One Dimensional (“1D”) “NMR” Data.
Kassambara, Alboukadel. 2025. ggpubr: “ggplot2” Based Publication Ready Plots. https://rpkgs.datanovia.com/ggpubr/.
Lê, Sébastien, Julie Josse, and François Husson. 2008. “FactoMineR: A Package for Multivariate Analysis.” Journal of Statistical Software 25 (1): 1–18. https://doi.org/10.18637/jss.v025.i01.
Madrid-Gambin, Francisco, Oller-Moreno, Sergio, Fernandez, Luis, Bartova, et al. 2020. “AlpsNMR: An r Package for Signal Processing of Fully Untargeted NMR-Based Metabolomics.” Bioinformatics, January. https://doi.org/10.1093/bioinformatics/btaa022.
Morgan, Martin. 2024. 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://bioconductor.github.io/BiocManager/.
Pedersen, Thomas Lin. 2025. ggraph: An Implementation of Grammar of Graphics for Graphs and Networks. https://ggraph.data-imaginist.com.
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. 2025. cascade: Contextualizing Untargeted Annotation with Semi-Quantitative Charged Aerosol Detection for Pertinent Characterization of Natural Extracts.
Rutz, Adriano, and Jean-Luc Wolfender. 2023. “Automated Composition Assessment of Natural Extracts: Untargeted Mass Spectrometry-Based Metabolite Profiling Integrating Semiquantitative Detection.” Journal of Agricultural and Food Chemistry 71 (46). https://doi.org/10.1021/acs.jafc.3c03099.
Sjoberg, David. 2020. ggbump: Bump Chart and Sigmoid Curves.
Slowikowski, Kamil. 2024. ggrepel: Automatically Position Non-Overlapping Text Labels with “ggplot2”. https://ggrepel.slowkow.com/.
Wickham, Hadley. 2011. “testthat: Get Started with Testing.” The R Journal 3: 5–10. https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.
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.
Wickham, Hadley, Winston Chang, Jim Hester, and Lionel Henry. 2024. pkgload: Simulate Package Installation and Attach. https://github.com/r-lib/pkgload.
Wickham, Hadley, Thomas Lin Pedersen, and Dana Seidel. 2025. scales: Scale Functions for Visualization. https://scales.r-lib.org.
Wilkins, David. 2023. treemapify: Draw Treemaps in “ggplot2”. https://wilkox.org/treemapify/.
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.