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tima

https://taxonomicallyinformedannotation.github.io/tima

https://github.com/taxonomicallyinformedannotation/tima

Science Score: 67.0%

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 115 DOI reference(s) in README
  • ✓
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    Links to: zenodo.org
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    Low similarity (16.4%) to scientific vocabulary

Keywords

chemotaxonomy lc-msms metabolite-annotation metabolomics natural-products scoring-system specialized-metabolome taxonomy
Last synced: 6 months ago · JSON representation ·

Repository

https://taxonomicallyinformedannotation.github.io/tima

Basic Info
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 5
  • Open Issues: 12
  • Releases: 30
Topics
chemotaxonomy lc-msms metabolite-annotation metabolomics natural-products scoring-system specialized-metabolome taxonomy
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Security Support Codemeta

README.md

tima

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

The initial work is available at https://doi.org/10.3389/fpls.2019.01329, with many improvements made since then. The workflow is illustrated below.

Workflow

This repository contains everything needed to perform Taxonomically Informed Metabolite Annotation.

Requirements

Here is what you minimally need:

  • A feature list (.csv) (see example features)
  • A spectral file corresponding to the feature list (.mgf) (see example spectra)
  • The biological source(s) of the sample(s) you are annotating (.csv) (see example metadata) (File is optional if only a single organism)

Optionally, you may want to add:

  • An in-house structure-organism pairs library (we provide LOTUS as starting point for each user)
  • Your own manual or automated annotations (we currently support annotations coming from SIRIUS (with some limitations))

Installation

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

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

Then, you should be able to install the rest with:

r tima::install()

Normally, everything you need should then be installed (as tested in here). If for some reason, some packages were not installed, try to install them manually. To avoid such issues, we offer a containerized version (see Docker).

Once installed, you are ready to go through our documentation, with the major steps detailed.

In case you do not have your data ready, you can obtain some example data using:

r tima::get_example_files()

Once you are done, you can open a small GUI to adapt your parameters and launch your job:

r tima::run_app()

This command will open a small app in your default browser.

Docker

A container is also available, together with a small compose file. Main commands are below:

``` bash docker pull adafede/tima-r

docker build . -t adafede/tima-r

```

``` bash docker run --user tima-user -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" -p 3838:3838 adafede/tima-r Rscript -e "tima::run_app()"

docker run --user tima-user -v "$(pwd)/.tima/data:/home/tima-user/.tima/data" adafede/tima-r Rscript -e "tima::tima_full()"

```

Main Citations

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

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

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

GNPS

General: https://doi.org/10.1038/nbt.3597

SIRIUS

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

Others

Additional software credits

| Package | Version | Citation | |:---|:---|:---| | archive | 1.1.12 | Hester and Csárdi (2025) | | base | 4.5.1 | R Core Team (2025) | | BiocManager | 1.30.26 | Morgan and Ramos (2025) | | BiocParallel | 1.43.4 | Wang et al. (2025) | | BiocVersion | 3.22.0 | Morgan (2025) | | docopt | 0.7.2 | de Jonge (2025) | | DT | 0.33 | Xie, Cheng, and Tan (2024) | | fs | 1.6.6 | Hester, Wickham, and Csárdi (2025) | | gt | 1.0.0 | Iannone et al. (2025) | | httr2 | 1.2.1 | Wickham (2025) | | igraph | 2.1.4 | Csardi and Nepusz (2006); Csárdi et al. (2025) | | IRanges | 2.43.0 | Lawrence et al. (2013) | | knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) | | logger | 0.4.0 | Daróczi and Wickham (2024) | | MetaboCoreUtils | 1.17.1 | Rainer et al. (2022a) | | MsBackendMgf | 1.17.0 | Gatto, Rainer, and Gibb (2025) | | MsBackendMsp | 1.13.0 | Rainer et al. (2022b) | | MsCoreUtils | 1.21.0 | Rainer et al. (2022c) | | msentropy | 0.1.4 | Li (2023) | | reticulate | 1.43.0 | Ushey, Allaire, and Tang (2025) | | rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) | | rotl | 3.1.0 | Michonneau, Brown, and Winter (2016); OpenTreeOfLife et al. (2019) | | shiny | 1.11.1 | Chang et al. (2025) | | shinybusy | 0.3.3 | Meyer and Perrier (2024) | | shinyhelper | 0.3.2 | Mason-Thom (2019) | | shinyjs | 2.1.0 | Attali (2021) | | shinytest2 | 0.4.1 | Schloerke (2025) | | shinyvalidate | 0.1.3 | Sievert, Iannone, and Cheng (2023) | | shinyWidgets | 0.9.0 | Perrier, Meyer, and Granjon (2025) | | Spectra | 1.19.4 | Rainer et al. (2022d) | | stringi | 1.8.7 | Gagolewski (2022) | | targets | 1.11.3 | Landau (2021) | | testthat | 3.2.3 | Wickham (2011) | | tidyfst | 1.8.2 | Huang and Zhao (2020) | | tidyselect | 1.2.1 | Henry and Wickham (2024) | | 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) | | visNetwork | 2.1.2 | Almende B.V. and Contributors and Thieurmel (2022) | | 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*. .
Almende B.V. and Contributors, and Benoit Thieurmel. 2022. *visNetwork: Network Visualization Using “vis.js” Library*. .
Attali, Dean. 2021. *shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds*. .
Chang, Winston, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke, Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert, and Barbara Borges. 2025. *shiny: Web Application Framework for r*. .
Csardi, Gabor, and Tamas Nepusz. 2006. “The Igraph Software Package for Complex Network Research.” *InterJournal* Complex Systems: 1695. .
Csárdi, Gábor, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, and Kirill Müller. 2025. *igraph: Network Analysis and Visualization in r*. .
Daróczi, Gergely, and Hadley Wickham. 2024. *logger: A Lightweight, Modern and Flexible Logging Utility*. .
de Jonge, Edwin. 2025. *docopt: Command-Line Interface Specification Language*. .
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. .
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*. .
Gatto, Laurent, Johannes Rainer, and Sebastian Gibb. 2025. *MsBackendMgf: Mass Spectrometry Data Backend for Mascot Generic Format (Mgf) Files*. .
Henry, Lionel, and Hadley Wickham. 2024. *tidyselect: Select from a Set of Strings*. .
Hester, Jim, and Gábor Csárdi. 2025. *archive: Multi-Format Archive and Compression Support*. .
Hester, Jim, Hadley Wickham, and Gábor Csárdi. 2025. *fs: Cross-Platform File System Operations Based on “libuv”*. .
Huang, Tian-Yuan, and Bin Zhao. 2020. “tidyfst: Tidy Verbs for Fast Data Manipulation.” *Journal of Open Source Software* 5 (52): 2388. .
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*. .
Landau, William Michael. 2021. “The Targets r Package: A Dynamic Make-Like Function-Oriented Pipeline Toolkit for Reproducibility and High-Performance Computing.” *Journal of Open Source Software* 6 (57): 2959. .
Lawrence, Michael, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, and Vincent Carey. 2013. “Software for Computing and Annotating Genomic Ranges.” *PLoS Computational Biology* 9. .
Li, Yuanyue. 2023. *msentropy: Spectral Entropy for Mass Spectrometry Data*. .
Mason-Thom, Chris. 2019. *shinyhelper: Easily Add Markdown Help Files to “shiny” App Elements*. .
Meyer, Fanny, and Victor Perrier. 2024. *shinybusy: Busy Indicators and Notifications for “Shiny” Applications*. .
Michonneau, Francois, Joseph W. Brown, and David J. Winter. 2016. “rotl: An r Package to Interact with the Open Tree of Life Data.” *Methods in Ecology and Evolution* 7 (12): 1476–81. .
Morgan, Martin. 2025. *BiocVersion: Set the Appropriate Version of Bioconductor Packages*. .
Morgan, Martin, and Marcel Ramos. 2025. *BiocManager: Access the Bioconductor Project Package Repository*. .
OpenTreeOfLife, Benjamin Redelings, Luna Luisa Sanchez Reyes, Karen A. Cranston, Jim Allman, Mark T. Holder, and Emily Jane McTavish. 2019. “Open Tree of Life Synthetic Tree.” Zenodo. .
Perrier, Victor, Fanny Meyer, and David Granjon. 2025. *shinyWidgets: Custom Inputs Widgets for Shiny*. .
R Core Team. 2025. *R: A Language and Environment for Statistical Computing*. Vienna, Austria: R Foundation for Statistical Computing. .
Rainer, Johannes, Andrea Vicini, Liesa Salzer, Jan Stanstrup, Josep M. Badia, Steffen Neumann, Michael A. Stravs, et al. 2022a. “A Modular and Expandable Ecosystem for Metabolomics Data Annotation in r.” *Metabolites* 12: 173. .
———, et al. 2022b. “A Modular and Expandable Ecosystem for Metabolomics Data Annotation in r.” *Metabolites* 12: 173. .
———, et al. 2022c. “A Modular and Expandable Ecosystem for Metabolomics Data Annotation in r.” *Metabolites* 12: 173. .
———, et al. 2022d. “A Modular and Expandable Ecosystem for Metabolomics Data Annotation in r.” *Metabolites* 12: 173. .
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. .
Schloerke, Barret. 2025. *Shinytest2: Testing for Shiny Applications*. .
Sievert, Carson, Richard Iannone, and Joe Cheng. 2023. *shinyvalidate: Input Validation for Shiny Apps*. .
Ushey, Kevin, JJ Allaire, and Yuan Tang. 2025. *reticulate: Interface to “Python”*. .
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. .
———. 2025. *Httr2: Perform HTTP Requests and Process the Responses*. .
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. .
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, Joe Cheng, and Xianying Tan. 2024. *DT: A Wrapper of the JavaScript Library “DataTables”*. .
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. *R Markdown Cookbook*. Boca Raton, Florida: Chapman; Hall/CRC. .

Owner

  • Name: taxonomicallyinformedannotation
  • Login: taxonomicallyinformedannotation
  • Kind: organization

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 "tima" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'tima: Taxonomically Informed Metabolite Annotation'
version: 2.12.0
doi: 10.5281/zenodo.5797920
identifiers:
- type: url
  value: https://taxonomicallyinformedannotation.github.io/tima
abstract: This package provides the infrastructure to perform Taxonomically Informed
  Metabolite Annotation.
authors:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
preferred-citation:
  type: manual
  title: 'tima: Taxonomically Informed Metabolite Annotation'
  authors:
  - family-names: Rutz
    given-names: Adriano
    email: adafede@gmail.com
    orcid: https://orcid.org/0000-0003-0443-9902
  - family-names: Allard
    given-names: Pierre-Marie
    email: pierre-marie.allard@unifr.ch
    orcid: https://orcid.org/0000-0003-3389-2191
  year: '2025'
  notes: R package, version 2.11.0
  doi: 10.5281/zenodo.5797920
repository: https://bioconductor.org/
repository-code: https://github.com/taxonomicallyinformedannotation/tima
url: https://taxonomicallyinformedannotation.github.io/tima-shinylive
contact:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
keywords:
- metaboliteAnnotation
- chemotaxonomy
- scoringSystem
- naturalProducts
- computationalMetabolomics
- taxonomicDistance
- specializedMetabolome
- lc-msms
- metabolite-annotation
- metabolomics
- natural-products
- scoring-system
- specialized-metabolome
- taxonomy
references:
- type: article
  title: Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  authors:
  - family-names: Rutz
    given-names: Adriano
    orcid: https://orcid.org/0000-0003-0443-9902
  - family-names: Dounoue-Kubo
    given-names: Miwa
  - family-names: Ollivier
    given-names: Simon
    orcid: https://orcid.org/0000-0002-7671-1736
  - family-names: Bisson
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  - family-names: Bagheri
    given-names: Mohsen
  - family-names: Saesong
    given-names: Tongchai
  - family-names: Ebrahimi
    given-names: Samad Nejad
    orcid: https://orcid.org/0000-0003-2167-8032
  - family-names: Ingkaninan
    given-names: Kornkanok
    orcid: https://orcid.org/0000-0002-4415-8489
  - family-names: Wolfender
    given-names: Jean-Luc
    orcid: https://orcid.org/0000-0002-0125-952X
  - family-names: Allard
    given-names: Pierre-Marie
    orcid: https://orcid.org/0000-0003-3389-2191
  journal: Frontiers in Plant Science
  year: '2019'
  volume: '10'
  url: https://doi.org/10.3389/fpls.2019.01329
  keywords:
  - metabolite annotation
  - chemotaxonomy
  - scoring system
  - natural products
  - computational metabolomics
  - taxonomic distance
  - specialized metabolome
  doi: 10.3389/FPLS.2019.01329
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  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
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  abstract: 'BiocParallel: Bioconductor facilities for parallel evaluation'
  notes: Imports
  url: https://github.com/Bioconductor/BiocParallel
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
    email: mtmorgan.bioc@gmail.com
  - family-names: Wang
    given-names: Jiefei
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
  - family-names: Thompson
    given-names: Ryan
    email: rct@thompsonclan.org
  - family-names: Turaga
    given-names: Nitesh
  year: '2025'
  doi: 10.18129/B9.bioc.BiocParallel
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  authors:
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    name-particle: de
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  authors:
  - family-names: Wickham
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  notes: Imports
  url: https://r.igraph.org/
  repository: https://CRAN.R-project.org/package=igraph
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
    orcid: https://orcid.org/0000-0001-7098-9676
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    given-names: Daniel
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2025'
  doi: 10.32614/CRAN.package.igraph
  version: '>= 2.1.4'
- type: software
  title: IRanges
  abstract: 'IRanges: Foundation of integer range manipulation in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/IRanges
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  - family-names: Aboyoun
    given-names: Patrick
  - family-names: Lawrence
    given-names: Michael
  year: '2025'
  doi: 10.18129/B9.bioc.IRanges
  version: '>= 2.40.1'
- type: software
  title: jsonlite
  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
  notes: Imports
  url: https://jeroen.r-universe.dev/jsonlite
  repository: https://CRAN.R-project.org/package=jsonlite
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2025'
  doi: 10.32614/CRAN.package.jsonlite
  version: '>= 2.0.0'
- type: software
  title: logger
  abstract: 'logger: A Lightweight, Modern and Flexible Logging Utility'
  notes: Imports
  url: https://daroczig.github.io/logger/
  repository: https://CRAN.R-project.org/package=logger
  authors:
  - family-names: Daróczi
    given-names: Gergely
    email: daroczig@rapporter.net
    orcid: https://orcid.org/0000-0003-3149-8537
  - 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.logger
  version: '>= 0.4.0'
- type: software
  title: methods
  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: MetaboCoreUtils
  abstract: 'MetaboCoreUtils: Core Utils for Metabolomics Data'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/MetaboCoreUtils
  repository: https://bioconductor.org/
  authors:
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Witting
    given-names: Michael
    email: michael.witting@helmholtz-muenchen.de
    orcid: https://orcid.org/0000-0002-1462-4426
  - family-names: Vicini
    given-names: Andrea
    email: andrea.vicini@eurac.edu
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  - family-names: Gine
    given-names: Roger
    email: alrgibe9@gmail.com
    orcid: https://orcid.org/0000-0003-0288-9619
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  doi: 10.18129/B9.bioc.MetaboCoreUtils
  version: '>= 1.14.0'
- type: software
  title: MsBackendMgf
  abstract: 'MsBackendMgf: Mass Spectrometry Data Backend for Mascot Generic Format
    (mgf) Files'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/MsBackendMgf
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  year: '2025'
  doi: 10.18129/B9.bioc.MsBackendMgf
  version: '>= 1.14.0'
- type: software
  title: MsBackendMsp
  abstract: 'MsBackendMsp: Mass Spectrometry Data Backend for NIST msp Files'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/MsBackendMsp
  repository: https://bioconductor.org/
  authors:
  - family-names: Steffen
    given-names: Neumann
    email: sneumann@ipb-halle.de
    orcid: https://orcid.org/0000-0002-7899-7192
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  year: '2025'
  doi: 10.18129/B9.bioc.MsBackendMsp
  version: '>= 1.10.0'
- type: software
  title: MsCoreUtils
  abstract: 'MsCoreUtils: Core Utils for Mass Spectrometry Data'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/MsCoreUtils
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  doi: 10.18129/B9.bioc.MsCoreUtils
  version: '>= 1.18.0'
- type: software
  title: msentropy
  abstract: 'msentropy: Spectral Entropy for Mass Spectrometry Data'
  notes: Imports
  url: https://github.com/YuanyueLi/MSEntropy
  repository: https://CRAN.R-project.org/package=msentropy
  authors:
  - family-names: Li
    given-names: Yuanyue
    email: liyuanyue@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.msentropy
  version: '>= 0.1.4'
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.purrr
  version: '>= 1.1.0'
- type: software
  title: reticulate
  abstract: 'reticulate: Interface to ''Python'''
  notes: Imports
  url: https://rstudio.github.io/reticulate/
  repository: https://CRAN.R-project.org/package=reticulate
  authors:
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Tang
    given-names: Yuan
    email: terrytangyuan@gmail.com
    orcid: https://orcid.org/0000-0001-5243-233X
  year: '2025'
  doi: 10.32614/CRAN.package.reticulate
  version: '>= 1.43.0'
- type: software
  title: rotl
  abstract: 'rotl: Interface to the ''Open Tree of Life'' API'
  notes: Imports
  url: https://docs.ropensci.org/rotl/
  repository: https://CRAN.R-project.org/package=rotl
  authors:
  - family-names: Michonneau
    given-names: Francois
    email: francois.michonneau@gmail.com
    orcid: https://orcid.org/0000-0002-9092-966X
  - family-names: Brown
    given-names: Joseph
    orcid: https://orcid.org/0000-0002-3835-8062
  - family-names: Winter
    given-names: David
    orcid: https://orcid.org/0000-0002-6165-0029
  year: '2025'
  doi: 10.32614/CRAN.package.rotl
  version: '>= 3.1.0'
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Imports
  url: https://shiny.posit.co/
  repository: https://CRAN.R-project.org/package=shiny
  authors:
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Sievert
    given-names: Carson
    email: carson@posit.co
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@posit.co
  - family-names: Allen
    given-names: Jeff
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2025'
  doi: 10.32614/CRAN.package.shiny
  version: '>= 1.11.1'
- type: software
  title: shinybusy
  abstract: 'shinybusy: Busy Indicators and Notifications for ''Shiny'' Applications'
  notes: Imports
  url: https://dreamrs.github.io/shinybusy/
  repository: https://CRAN.R-project.org/package=shinybusy
  authors:
  - family-names: Meyer
    given-names: Fanny
  - family-names: Perrier
    given-names: Victor
    email: victor.perrier@dreamrs.fr
  year: '2025'
  doi: 10.32614/CRAN.package.shinybusy
  version: '>= 0.3.3'
- type: software
  title: shinyWidgets
  abstract: 'shinyWidgets: Custom Inputs Widgets for Shiny'
  notes: Imports
  url: https://dreamrs.github.io/shinyWidgets/
  repository: https://CRAN.R-project.org/package=shinyWidgets
  authors:
  - family-names: Perrier
    given-names: Victor
    email: victor.perrier@dreamrs.fr
  - family-names: Meyer
    given-names: Fanny
  - family-names: Granjon
    given-names: David
  year: '2025'
  doi: 10.32614/CRAN.package.shinyWidgets
  version: '>= 0.9.0'
- type: software
  title: Spectra
  abstract: 'Spectra: Spectra Infrastructure for Mass Spectrometry Data'
  notes: Imports
  url: https://github.com/RforMassSpectrometry/Spectra
  repository: https://bioconductor.org/
  authors:
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gibb
    given-names: Sebastian
    email: mail@sebastiangibb.de
    orcid: https://orcid.org/0000-0001-7406-4443
  - family-names: Louail
    given-names: Philippine
    email: philippine.louail@eurac.edu
    orcid: https://orcid.org/0009-0007-5429-6846
  year: '2025'
  doi: 10.18129/B9.bioc.Spectra
  version: '>= 1.16.1'
- type: software
  title: stats
  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: 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: targets
  abstract: 'targets: Dynamic Function-Oriented ''Make''-Like Declarative Pipelines'
  notes: Imports
  url: https://docs.ropensci.org/targets/
  repository: https://CRAN.R-project.org/package=targets
  authors:
  - family-names: Landau
    given-names: William Michael
    email: will.landau.oss@gmail.com
    orcid: https://orcid.org/0000-0003-1878-3253
  year: '2025'
  doi: 10.32614/CRAN.package.targets
  version: '>= 1.11.3'
- type: software
  title: tidyfst
  abstract: 'tidyfst: Tidy Verbs for Fast Data Manipulation'
  notes: Imports
  url: https://hope-data-science.github.io/tidyfst/
  repository: https://CRAN.R-project.org/package=tidyfst
  authors:
  - family-names: Huang
    given-names: Tian-Yuan
    email: huang.tian-yuan@qq.com
    orcid: https://orcid.org/0000-0002-4151-3764
  year: '2025'
  doi: 10.32614/CRAN.package.tidyfst
  version: '>= 1.8.2'
- type: software
  title: tidyselect
  abstract: 'tidyselect: Select from a Set of Strings'
  notes: Imports
  url: https://tidyselect.r-lib.org
  repository: https://CRAN.R-project.org/package=tidyselect
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.tidyselect
  version: '>= 1.2.1'
- 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: 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: visNetwork
  abstract: 'visNetwork: Network Visualization using ''vis.js'' Library'
  notes: Imports
  url: https://datastorm-open.github.io/visNetwork/
  repository: https://CRAN.R-project.org/package=visNetwork
  authors:
  - name: Almende B.V. and Contributors
    website: https://visjs.org/
  - family-names: Thieurmel
    given-names: Benoit
    email: bthieurmel@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.visNetwork
  version: '>= 2.1.2'
- type: software
  title: yaml
  abstract: 'yaml: Methods to Convert R Data to YAML and Back'
  notes: Imports
  url: https://github.com/vubiostat/r-yaml/
  repository: https://CRAN.R-project.org/package=yaml
  authors:
  - family-names: Garbett
    given-names: Shawn P
  - family-names: Stephens
    given-names: Jeremy
  - family-names: Simonov
    given-names: Kirill
  - family-names: Xie
    given-names: Yihui
  - family-names: Dong
    given-names: Zhuoer
  - family-names: Wickham
    given-names: Hadley
  - family-names: Horner
    given-names: Jeffrey
  - name: reikoch
  - family-names: Beasley
    given-names: Will
  - family-names: O'Connor
    given-names: Brendan
  - family-names: Warnes
    given-names: Gregory R.
  - family-names: Quinn
    given-names: Michael
  - family-names: Kamvar
    given-names: Zhian N.
  - family-names: Gao
    given-names: Charlie
  year: '2025'
  doi: 10.32614/CRAN.package.yaml
  version: '>= 2.3.10'
- 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: 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: pkgload
  abstract: 'pkgload: Simulate Package Installation and Attach'
  notes: Suggests
  url: https://pkgload.r-lib.org
  repository: https://CRAN.R-project.org/package=pkgload
  authors:
  - family-names: Wickham
    given-names: Hadley
  - family-names: Chang
    given-names: Winston
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.pkgload
  version: '>= 1.4.0'
- 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: R.utils
  abstract: 'R.utils: Various Programming Utilities'
  notes: Suggests
  url: https://henrikbengtsson.github.io/R.utils/
  repository: https://CRAN.R-project.org/package=R.utils
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2025'
  doi: 10.32614/CRAN.package.R.utils
  version: '>= 2.13.0'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Suggests
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
  version: '>= 1.1.6'
- type: software
  title: shinyhelper
  abstract: 'shinyhelper: Easily Add Markdown Help Files to ''shiny'' App Elements'
  notes: Suggests
  url: https://github.com/cwthom/shinyhelper
  repository: https://CRAN.R-project.org/package=shinyhelper
  authors:
  - family-names: Mason-Thom
    given-names: Chris
    email: christopher.w.thom@outlook.com
  year: '2025'
  doi: 10.32614/CRAN.package.shinyhelper
  version: '>= 0.3.2'
- type: software
  title: shinyjs
  abstract: 'shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds'
  notes: Suggests
  url: https://deanattali.com/shinyjs/
  repository: https://CRAN.R-project.org/package=shinyjs
  authors:
  - family-names: Attali
    given-names: Dean
    email: daattali@gmail.com
    orcid: https://orcid.org/0000-0002-5645-3493
  year: '2025'
  doi: 10.32614/CRAN.package.shinyjs
  version: '>= 2.1.0'
- type: software
  title: shinytest2
  abstract: 'shinytest2: Testing for Shiny Applications'
  notes: Suggests
  url: https://rstudio.github.io/shinytest2/
  repository: https://CRAN.R-project.org/package=shinytest2
  authors:
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    "SystemRequirements": "\n    python (< 3.14,>= 3.10)"
  },
  "keywords": [
    "metaboliteAnnotation",
    "chemotaxonomy",
    "scoringSystem",
    "naturalProducts",
    "computationalMetabolomics",
    "taxonomicDistance",
    "specializedMetabolome",
    "lc-msms",
    "metabolite-annotation",
    "metabolomics",
    "natural-products",
    "scoring-system",
    "taxonomy",
    "specialized-metabolome",
    "r"
  ],
  "fileSize": "2572.569KB",
  "citation": [
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2025",
      "author": [
        {
          "@type": "Person",
          "givenName": "Adriano",
          "familyName": "Rutz",
          "email": "adafede@gmail.com",
          "@id": "https://orcid.org/0000-0003-0443-9902"
        }
      ],
      "name": "tima: Taxonomically Informed Metabolite Annotation",
      "identifier": "10.5281/zenodo.5797920",
      "description": "R package, version 2.11.0",
      "@id": "https://doi.org/10.5281/zenodo.5797920",
      "sameAs": "https://doi.org/10.5281/zenodo.5797920"
    },
    {
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      "datePublished": "2019",
      "author": [
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          "givenName": "Adriano",
          "familyName": "Rutz",
          "@id": "https://orcid.org/0000-0003-0443-9902"
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          "@id": "https://orcid.org/0000-0002-7671-1736"
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          "givenName": "Jonathan",
          "familyName": "Bisson",
          "@id": "https://orcid.org/0000-0003-1640-9989"
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        {
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          "@id": "https://orcid.org/0000-0003-2167-8032"
        },
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          "givenName": "Kornkanok",
          "familyName": "Ingkaninan",
          "@id": "https://orcid.org/0000-0002-4415-8489"
        },
        {
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          "givenName": "Jean-Luc",
          "familyName": "Wolfender",
          "@id": "https://orcid.org/0000-0002-0125-952X"
        },
        {
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          "givenName": "Pierre-Marie",
          "familyName": "Allard",
          "@id": "https://orcid.org/0000-0003-3389-2191"
        }
      ],
      "name": "Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation",
      "identifier": "10.3389/FPLS.2019.01329",
      "url": "https://doi.org/10.3389/fpls.2019.01329",
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      "isPartOf": {
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        "datePublished": "2019",
        "isPartOf": {
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            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "10",
          "name": "Frontiers in Plant Science"
        }
      }
    }
  ],
  "releaseNotes": "https://github.com/taxonomicallyinformedannotation/tima/blob/main/NEWS.md",
  "readme": "https://github.com/taxonomicallyinformedannotation/tima/blob/main/README.md",
  "contIntegration": [
    "https://github.com/taxonomicallyinformedannotation/tima/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/taxonomicallyinformedannotation/tima"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
}

GitHub Events

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Last Year
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  • Watch event: 1
  • Delete event: 7
  • Issue comment event: 34
  • Push event: 591
  • Pull request event: 17
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 14
  • Total pull requests: 3
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  • Average time to close pull requests: 14 minutes
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.21
  • Average comments per pull request: 0.0
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  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 12
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  • Average comments per pull request: 0.0
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Top Authors
Issue Authors
  • Adafede (12)
  • TOTOZAFY (2)
  • AndreaCa96 (1)
  • RemyMG (1)
Pull Request Authors
  • renovate[bot] (13)
  • Adafede (2)
  • dependabot[bot] (1)
Top Labels
Issue Labels
feature (4) breaking change :skull_and_crossbones: (1) upkeep (1)
Pull Request Labels
dependencies (1) github_actions (1)

Dependencies

DESCRIPTION cran
  • R >= 4.1.0 depends
  • crayon * imports
  • curl * imports
  • data.table * imports
  • docopt * imports
  • dplyr * imports
  • glue * imports
  • lifecycle * imports
  • purrr * imports
  • readr * imports
  • rlang >= 0.4.11 imports
  • rotl * imports
  • splitstackshape * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • yaml * imports
  • covr * suggests
  • knitr >= 1.1.0 suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat >= 3.0.0 suggests
  • utils * suggests
.github/workflows/carbonate.yaml actions
  • callmekatootie/carbonate v1.0.2 composite
.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/clear_cache.yml actions
  • actions/github-script v6 composite
.github/workflows/docker.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
.github/workflows/link_check.yaml actions
  • actions/checkout master composite
  • gaurav-nelson/github-action-markdown-link-check v1 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pr-commands.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/remove-old-artifacts.yml actions
  • c-hive/gha-remove-artifacts v1 composite
.github/workflows/sitemap-generation.yml actions
  • actions/checkout v3 composite
  • cicirello/generate-sitemap v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/tima.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/versioning.yml actions
  • Actions-R-Us/actions-tagger latest composite
Dockerfile docker
  • ghcr.io/bioconductor/bioconductor RELEASE_3_16 build
docker-compose.yml docker
  • adafede/tima-r latest