Science Score: 67.0%
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✓DOI references
Found 77 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Keywords
charged-aerosol-detector
chemical-composition
lc-msms
metabolite-annotation
metabolomics
natural-extracts
natural-products
Last synced: 10 months ago
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JSON representation
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Repository
https://adafede.github.io/cascade
Basic Info
- Host: GitHub
- Owner: Adafede
- License: agpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://adafede.github.io/cascade/
- Size: 160 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 1
- Releases: 1
Topics
charged-aerosol-detector
chemical-composition
lc-msms
metabolite-annotation
metabolomics
natural-extracts
natural-products
Created over 4 years ago
· Last pushed 10 months ago
Metadata Files
Readme
Changelog
Contributing
License
Code of conduct
Citation
Security
Support
Codemeta
README.md
CASCADE 
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Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts.
⚠️ This repository is not maintained and will not be except for extreme interest. It has just been opened for the sake of transparency.
The initial work is available at https://doi.org/10.1021/acs.jafc.3c03099, with some improvements made since then. The workflow is illustrated below.
Requirements
Here is what you minimally need:
- A file
(.mzML)
containing DDA
MS
data with an additional detector
(PDA,
ELSD,
CAD)
- In case you don’t know how to obtain it, see: wiki/How-to-create-a-compliant-mzML-file
- A file (.csv) containing features, as obtained by mzmine
- A file (.tsv) containing annotations, as obtained by TIMA
Installation
As the package is not (yet) available on CRAN, you will need to install with:
r
install.packages(
"cascade",
repos = c(
"https://adafede.r-universe.dev",
"https://bioc.r-universe.dev",
"https://cloud.r-project.org"
)
)
Once installed, you are ready to go through our documentation, with the major steps detailed.
Main Citations
CASCADE
https://doi.org/10.1021/acs.jafc.3c03099
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
- CSI:FingerId: https://doi.org/10.1073/pnas.1509788112
- ZODIAC: https://doi.org/10.1038/s42256-020-00234-6
- CANOPUS: https://doi.org/10.1038/s41587-020-0740-8
- COSMIC: https://doi.org/10.1038/s41587-021-01045-9
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
- NPClassifier: https://doi.org/10.1021/acs.jnatprod.1c00399
Additional software credits
| Package | Version | Citation | |:---|:---|:---| | base | 4.5.1 | R Core Team (2025) | | baseline | 1.3.7 | Liland, Almøy, and Mevik (2010); Liland and Mevik (2025) | | BiocManager | 1.30.26 | Morgan and Ramos (2025) | | BiocParallel | 1.43.4 | Wang et al. (2025) | | BiocVersion | 3.22.0 | Morgan (2025) | | cascade | 0.0.0.9001 | Rutz and Wolfender (2023); Rutz (2025) | | caTools | 1.18.3 | Tuszynski (2024) | | data.table | 1.17.8 | Barrett et al. (2025) | | gt | 1.0.0 | Iannone et al. (2025) | | htmltools | 0.5.8.1 | Cheng et al. (2024) | | knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) | | MSnbase | 2.35.0 | Gatto and Lilley (2012); Gatto, Gibb, and Rainer (2020) | | mzR | 2.43.1 | Pedrioli et al. (2004); Keller et al. (2005); Kessner et al. (2008); Martens et al. (2010); Chambers et al. (2012) | | pkgload | 1.4.0 | Wickham et al. (2024) | | plotly | 4.11.0 | Sievert (2020) | | R.utils | 2.13.0 | Bengtsson (2025) | | rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) | | 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) | | tima | 2.12.0 | Rutz et al. (2019); Rutz and Allard (2025) | | WikidataQueryServiceR | 1.0.0 | Popov (2020) |
Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier
Luraschi, Kevin Ushey, Aron Atkins, et al. 2024.
*rmarkdown: Dynamic Documents for r*.
.
Barrett, Tyson, Matt Dowle, Arun Srinivasan, Jan Gorecki, Michael
Chirico, Toby Hocking, Benjamin Schwendinger, and Ivan Krylov. 2025.
*data.table: Extension of
“data.frame”*.
.
Bengtsson, Henrik. 2025. *R.utils: Various
Programming Utilities*. .
Chambers, Matthew C., Maclean, Brendan, Burke, Robert, Amodei, et al.
2012. “A cross-platform toolkit for mass
spectrometry and proteomics.” *Nat Biotech* 30 (10): 918–20.
.
Cheng, Joe, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie,
and Jeff Allen. 2024. *htmltools: Tools for
HTML*. .
Fairbanks, Mark. 2024. *tidytable: Tidy
Interface to “data.table”*.
.
Gagolewski, Marek. 2022. “stringi: Fast and
Portable Character String Processing in R.” *Journal of Statistical
Software* 103 (2): 1–59. .
Gatto, Laurent, Sebastian Gibb, and Johannes Rainer. 2020. “MSnbase,
Efficient and Elegant r-Based Processing and Visualisation of Raw Mass
Spectrometry Data.” *bioRxiv*.
Gatto, Laurent, and Kathryn Lilley. 2012. “MSnbase - an r/Bioconductor
Package for Isobaric Tagged Mass Spectrometry Data Visualization,
Processing and Quantitation.” *Bioinformatics* 28: 288–89.
Iannone, Richard, Joe Cheng, Barret Schloerke, Ellis Hughes, Alexandra
Lauer, JooYoung Seo, Ken Brevoort, and Olivier Roy. 2025.
*gt: Easily Create Presentation-Ready
Display Tables*. .
Keller, Andrew, Jimmy Eng, Ning Zhang, Xiao-jun Li, and Ruedi Aebersold.
2005. “A Uniform Proteomics MS/MS Analysis Platform Utilizing Open XML
File Formats.” *Mol Syst Biol*.
Kessner, Darren, Matt Chambers, Robert Burke, David Agus, and Parag
Mallick. 2008. “ProteoWizard: Open Source Software for Rapid Proteomics
Tools Development.” *Bioinformatics* 24 (21): 2534–36.
.
Liland, Kristian Hovde, Trygve Almøy, and Bjørn-Helge Mevik. 2010.
“Optimal Choice of Baseline Correction for Multivariate Calibration of
Spectra.” *Applied Spectroscopy* 64: 1007–16.
.
Liland, Kristian Hovde, and Bjørn-Helge Mevik. 2025.
*baseline: Baseline Correction of Spectra*.
.
Martens, Lennart, Matthew Chambers, Marc Sturm, Darren Kessner, Fredrik
Levander, Jim Shofstahl, Wilfred H Tang, et al. 2010. “MzML - a
Community Standard for Mass Spectrometry Data.” *Mol Cell Proteomics*.
.
Morgan, Martin. 2025. *BiocVersion: Set the Appropriate Version of
Bioconductor Packages*. .
Morgan, Martin, and Marcel Ramos. 2025. *BiocManager: Access the
Bioconductor Project Package Repository*.
.
Pedrioli, Patrick G A, Jimmy K Eng, Robert Hubley, Mathijs Vogelzang,
Eric W Deutsch, Brian Raught, Brian Pratt, et al. 2004. “A Common Open
Representation of Mass Spectrometry Data and Its Application to
Proteomics Research.” *Nat Biotechnol* 22 (11): 1459–66.
.
Popov, Mikhail. 2020. *WikidataQueryServiceR: API Client Library for
“Wikidata Query Service”*.
.
R Core Team. 2025. *R: A Language and Environment for Statistical
Computing*. Vienna, Austria: R Foundation for Statistical Computing.
Rutz, Adriano. 2025. *cascade:
Contextualizing Untargeted Annotation with Semi-Quantitative Charged
Aerosol Detection for Pertinent Characterization of Natural Extracts*.
Rutz, Adriano, and Pierre-Marie Allard. 2025.
*tima: Taxonomically Informed Metabolite
Annotation*. .
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.
.
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).
.
Sievert, Carson. 2020. *Interactive Web-Based Data Visualization with r,
Plotly, and Shiny*. Chapman; Hall/CRC. .
Tuszynski, Jarek. 2024. *caTools: Tools:
Moving Window Statistics, GIF, Base64, ROC AUC, Etc*.
.
Wang, Jiefei, Martin Morgan, Valerie Obenchain, Michel Lang, Ryan
Thompson, and Nitesh Turaga. 2025. *BiocParallel: Bioconductor
Facilities for Parallel Evaluation*.
.
Wickham, Hadley. 2011. “testthat: Get
Started with Testing.” *The R Journal* 3: 5–10.
.
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. .
Wickham, Hadley, Winston Chang, Jim Hester, and Lionel Henry. 2024.
*pkgload: Simulate Package Installation and
Attach*. .
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.
———. 2025. *knitr: A General-Purpose Package
for Dynamic Report Generation in R*.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. *R Markdown: The
Definitive Guide*. Boca Raton, Florida: Chapman; Hall/CRC.
.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. *R Markdown
Cookbook*. Boca Raton, Florida: Chapman; Hall/CRC.
.
Owner
- Name: Adriano Rutz
- Login: Adafede
- Kind: user
- Location: Zürich, Switzerland
- Website: https://adafede.github.io/
- Repositories: 10
- Profile: https://github.com/Adafede
Pharmacist | Computational Metabolomics
Citation (CITATION.cff)
# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
cff-version: 1.2.0
message: 'To cite package "cascade" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'cascade: Contextualizing untargeted Annotation with Semi-quantitative Charged
Aerosol Detection for pertinent characterization of natural Extracts'
version: 0.0.0.9001
abstract: This package provides the infrastructure to perform Automated Composition
Assessment of Natural Extracts.
authors:
- family-names: Rutz
given-names: Adriano
email: adafede@gmail.com
orcid: https://orcid.org/0000-0003-0443-9902
preferred-citation:
type: manual
title: 'cascade: Contextualizing untargeted Annotation with Semi-quantitative Charged
Aerosol Detection for pertinent characterization of natural Extracts'
authors:
- family-names: Rutz
given-names: Adriano
email: adafede@gmail.com
orcid: https://orcid.org/0000-0003-0443-9902
year: '2025'
notes: R package, version 0.0.9001
repository: https://bioconductor.org/
repository-code: https://github.com/adafede/cascade
url: https://adafede.github.io/cascade
contact:
- family-names: Rutz
given-names: Adriano
email: adafede@gmail.com
orcid: https://orcid.org/0000-0003-0443-9902
keywords:
- metaboliteAnnotation
- chargedAerosolDetector
- semiQuantitative
- naturalProducts
- computationalMetabolomics
- specializedMetabolome
- charged-aerosol-detector
- chemical-composition
- lc-msms
- metabolite-annotation
- metabolomics
- natural-extracts
- natural-products
references:
- type: article
title: 'Automated Composition Assessment of Natural Extracts: Untargeted Mass Spectrometry-Based
Metabolite Profiling Integrating Semiquantitative Detection'
authors:
- family-names: Rutz
given-names: Adriano
orcid: https://orcid.org/0000-0003-0443-9902
- family-names: Wolfender
given-names: Jean-Luc
orcid: https://orcid.org/0000-0002-0125-952X
journal: Journal of Agricultural and Food Chemistry
year: '2023'
volume: '71'
issue: '46'
url: https://doi.org/10.1021/acs.jafc.3c03099
keywords:
- metabolite annotation
- charged aerosol detector
- semi-quantitative
- natural products
- computational metabolomics
- specialized metabolome
doi: 10.1021/acs.jafc.3c03099
issn: 1664-462X
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notes: Depends
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address: Vienna, Austria
year: '2025'
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abstract: 'baseline: Baseline Correction of Spectra'
notes: Imports
url: https://github.com/khliland/baseline/
repository: https://CRAN.R-project.org/package=baseline
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notes: Imports
url: https://r-datatable.com
repository: https://CRAN.R-project.org/package=data.table
authors:
- family-names: Barrett
given-names: Tyson
email: t.barrett88@gmail.com
orcid: https://orcid.org/0000-0002-2137-1391
- family-names: Dowle
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email: mattjdowle@gmail.com
- family-names: Srinivasan
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email: asrini@pm.me
- family-names: Gorecki
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- family-names: Chirico
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repository: https://CRAN.R-project.org/package=forcats
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repository: https://CRAN.R-project.org/package=purrr
authors:
- family-names: Wickham
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repository: https://CRAN.R-project.org/package=R.utils
authors:
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given-names: Henrik
email: henrikb@braju.com
year: '2025'
doi: 10.32614/CRAN.package.R.utils
version: '>= 2.13.0'
- type: software
title: stringi
abstract: 'stringi: Fast and Portable Character String Processing Facilities'
notes: Imports
url: https://stringi.gagolewski.com/
repository: https://CRAN.R-project.org/package=stringi
authors:
- family-names: Gagolewski
given-names: Marek
email: marek@gagolewski.com
orcid: https://orcid.org/0000-0003-0637-6028
year: '2025'
doi: 10.32614/CRAN.package.stringi
version: '>= 1.8.7'
- type: software
title: tibble
abstract: 'tibble: Simple Data Frames'
notes: Imports
url: https://tibble.tidyverse.org/
repository: https://CRAN.R-project.org/package=tibble
authors:
- family-names: Müller
given-names: Kirill
email: kirill@cynkra.com
orcid: https://orcid.org/0000-0002-1416-3412
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
year: '2025'
doi: 10.32614/CRAN.package.tibble
version: '>= 3.3.0'
- type: software
title: tidytable
abstract: 'tidytable: Tidy Interface to ''data.table'''
notes: Imports
url: https://markfairbanks.github.io/tidytable/
repository: https://CRAN.R-project.org/package=tidytable
authors:
- family-names: Fairbanks
given-names: Mark
email: mark.t.fairbanks@gmail.com
year: '2025'
doi: 10.32614/CRAN.package.tidytable
version: '>= 0.11.2'
- type: software
title: tima
abstract: 'tima: Taxonomically Informed Metabolite Annotation'
notes: Imports
url: https://taxonomicallyinformedannotation.github.io/tima-shinylive
repository: https://bioconductor.org/
authors:
- family-names: Rutz
given-names: Adriano
email: adafede@gmail.com
orcid: https://orcid.org/0000-0003-0443-9902
year: '2025'
version: '>= 2.12.0'
- type: software
title: utils
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
- type: software
title: WikidataQueryServiceR
abstract: 'WikidataQueryServiceR: API Client Library for ''Wikidata Query Service'''
notes: Imports
url: https://github.com/bearloga/WikidataQueryServiceR
repository: https://CRAN.R-project.org/package=WikidataQueryServiceR
authors:
- family-names: Popov
given-names: Mikhail
email: mikhail@wikimedia.org
year: '2025'
doi: 10.32614/CRAN.package.WikidataQueryServiceR
version: '>= 1.0.0'
- type: software
title: altdoc
abstract: 'altdoc: Package Documentation Websites with ''Quarto'', ''Docsify'',
''Docute'', or ''MkDocs'''
notes: Suggests
url: https://altdoc.etiennebacher.com
repository: https://CRAN.R-project.org/package=altdoc
authors:
- family-names: Bacher
given-names: Etienne
email: etienne.bacher@protonmail.com
- family-names: Arel-Bundock
given-names: Vincent
email: vincent.arel-bundock@umontreal.ca
orcid: https://orcid.org/0000-0003-2042-7063
year: '2025'
doi: 10.32614/CRAN.package.altdoc
version: '>= 0.5.0'
- type: software
title: BiocManager
abstract: 'BiocManager: Access the Bioconductor Project Package Repository'
notes: Suggests
url: https://bioconductor.github.io/BiocManager/
repository: https://CRAN.R-project.org/package=BiocManager
authors:
- family-names: Morgan
given-names: Martin
email: martin.morgan@roswellpark.org
orcid: https://orcid.org/0000-0002-5874-8148
- family-names: Ramos
given-names: Marcel
email: marcel.ramos@sph.cuny.edu
orcid: https://orcid.org/0000-0002-3242-0582
year: '2025'
doi: 10.32614/CRAN.package.BiocManager
version: '>= 1.30.25'
- type: software
title: BiocVersion
abstract: 'BiocVersion: Set the appropriate version of Bioconductor packages'
notes: Suggests
repository: https://bioconductor.org/
authors:
- family-names: Morgan
given-names: Martin
email: martin.morgan@roswellpark.org
year: '2025'
doi: 10.18129/B9.bioc.BiocVersion
version: '>= 3.20.0'
- type: software
title: grateful
abstract: 'grateful: Facilitate Citation of R Packages'
notes: Suggests
url: https://pakillo.github.io/grateful/
repository: https://CRAN.R-project.org/package=grateful
authors:
- family-names: Rodriguez-Sanchez
given-names: Francisco
email: f.rodriguez.sanc@gmail.com
orcid: https://orcid.org/0000-0002-7981-1599
- family-names: Jackson
given-names: Connor P.
email: connor@cpjackson.net
orcid: https://orcid.org/0000-0002-4220-5210
year: '2025'
doi: 10.32614/CRAN.package.grateful
version: '>= 0.2.12'
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2025'
doi: 10.32614/CRAN.package.knitr
version: '>= 1.50'
- type: software
title: quarto
abstract: 'quarto: R Interface to ''Quarto'' Markdown Publishing System'
notes: Suggests
url: https://quarto-dev.github.io/quarto-r/
repository: https://CRAN.R-project.org/package=quarto
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
orcid: https://orcid.org/0000-0003-0174-9868
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
year: '2025'
doi: 10.32614/CRAN.package.quarto
version: '>= 1.4.4'
- type: software
title: lifecycle
abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
notes: Suggests
url: https://lifecycle.r-lib.org/
repository: https://CRAN.R-project.org/package=lifecycle
authors:
- family-names: Henry
given-names: Lionel
email: lionel@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
orcid: https://orcid.org/0000-0003-4757-117X
year: '2025'
doi: 10.32614/CRAN.package.lifecycle
version: '>= 1.0.4'
- type: software
title: spelling
abstract: 'spelling: Tools for Spell Checking in R'
notes: Suggests
url: https://ropensci.r-universe.dev/spelling
repository: https://CRAN.R-project.org/package=spelling
authors:
- family-names: Ooms
given-names: Jeroen
email: jeroenooms@gmail.com
orcid: https://orcid.org/0000-0002-4035-0289
- family-names: Hester
given-names: Jim
email: james.hester@rstudio.com
year: '2025'
doi: 10.32614/CRAN.package.spelling
version: '>= 2.3.1'
- type: software
title: svglite
abstract: 'svglite: An ''SVG'' Graphics Device'
notes: Suggests
url: https://svglite.r-lib.org
repository: https://CRAN.R-project.org/package=svglite
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Henry
given-names: Lionel
email: lionel@posit.co
- family-names: Pedersen
given-names: Thomas Lin
email: thomas.pedersen@posit.co
orcid: https://orcid.org/0000-0002-5147-4711
- family-names: Luciani
given-names: T Jake
email: jake@apache.org
- family-names: Decorde
given-names: Matthieu
email: matthieu.decorde@ens-lyon.fr
- family-names: Lise
given-names: Vaudor
email: lise.vaudor@ens-lyon.fr
year: '2025'
doi: 10.32614/CRAN.package.svglite
version: '>= 2.2.1'
- type: software
title: testthat
abstract: 'testthat: Unit Testing for R'
notes: Suggests
url: https://testthat.r-lib.org
repository: https://CRAN.R-project.org/package=testthat
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2025'
doi: 10.32614/CRAN.package.testthat
version: '>= 3.0.0'
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],
"releaseNotes": "https://github.com/adafede/cascade/blob/main/NEWS.md",
"readme": "https://github.com/Adafede/cascade/blob/main/README.md",
"contIntegration": [
"https://github.com/adafede/cascade/actions/workflows/R-CMD-check.yaml",
"https://app.codecov.io/gh/adafede/cascade"
],
"developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
}GitHub Events
Total
- Release event: 2
- Delete event: 7
- Push event: 308
- Gollum event: 2
- Pull request event: 15
- Create event: 10
Last Year
- Release event: 2
- Delete event: 7
- Push event: 308
- Gollum event: 2
- Pull request event: 15
- Create event: 10