centroidr

https://adafede.github.io/CentroidR

https://github.com/adafede/centroidr

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 24 DOI reference(s) in README
○
Academic publication links
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Academic email domains
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Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary

Keywords

centroid centroiding mass-spectra mass-spectrometry

Last synced: 6 months ago · JSON representation ·

Repository

https://adafede.github.io/CentroidR

Basic Info

Host: GitHub
Owner: Adafede
License: agpl-3.0
Language: R
Default Branch: main
Homepage: https://adafede.github.io/CentroidR/
Size: 1.71 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 2
Releases: 0

Topics

centroid centroiding mass-spectra mass-spectrometry

Created about 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation Codemeta

CentroidR

Repository to centroid profile spectra.

This repository is experimental. Use it at your own risks. Inspired from the original work at https://github.com/EuracBiomedicalResearch/batch_centroid

Requirements

Here is what you minimally need:

An mzML file containing profile spectra

Here is a generic command in case:

bash docker run -it --rm -e WINEDEBUG=-all -v .:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert "path_to_your/raw/spectra.wiff" --ignoreUnknownInstrumentError

Note: If using Sciex raw format, you can use both the .wiff and the .wiff2 format for this step.

Installation

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

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

Use

Single file

r CentroidR::centroid_one_file(file = "path_to_your/profile/spectra.mzML", pattern = "/profile/", replacement = "/profile_centroided/")

bash Rscript inst/scripts/centroiding.R --file "path_to_your/profile/spectra.mzML" --pattern "/profile/" --replacement "/profile_centroided/"

Multiple files

r "path_to_your/profiles/" |> list.files(pattern = ".mzML", full.names = TRUE) |> purrr::walk( .f = CentroidR::centroid_one_file, pattern = "/profiles/", replacement = "/profiles_centroided/", .progress = TRUE)

bash Rscript inst/scripts/centroiding.R --directory "path_to_your/profiles/" --pattern "/profiles/" --replacement "/profiles_centroided/"

bash Rscript inst/scripts/centroiding.R --help

Docker

``` bash docker pull adafede/centroidr

docker build . -t adafede/centroidr

```

bash docker run --rm \ -v path_to_your:/home \ adafede/centroidr \ Rscript centroiding.R --file "home/profile/spectra.mzML" --pattern "/profile/" --replacement "/profile_centroided/"

bash docker run --rm \ -v path_to_your:/home \ adafede/centroidr \ Rscript centroiding.R --directory "home/profiles/" --pattern "/profiles/" --replacement "/profiles_centroided/"

To see all parameters

bash docker run --rm \ -v path_to_your:/home \ adafede/centroidr \ Rscript centroiding.R --help

Citation

TODO

Additional software credits

| Package | Version | Citation | |:---|:---|:---| | 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) | | CentroidR | 0.0.0.9001 | Rutz and Rainer (2025) | | knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) | | logger | 0.4.0 | Daróczi and Wickham (2024) | | MsCoreUtils | 1.21.0 | Rainer et al. (2022a) | | mzR | 2.43.1 | Pedrioli et al. (2004); Keller et al. (2005); Kessner et al. (2008); Martens et al. (2010); Chambers et al. (2012) | | optparse | 1.7.5 | Davis (2024) | | rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) | | Spectra | 1.19.4 | Rainer et al. (2022b) | | testthat | 3.2.3 | Wickham (2011) | | tidyverse | 2.0.0 | Wickham et al. (2019) |

Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. *rmarkdown: Dynamic Documents for r*. .

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. .

Daróczi, Gergely, and Hadley Wickham. 2024. *logger: A Lightweight, Modern and Flexible Logging Utility*. .

Davis, Trevor L. 2024. *optparse: Command Line Option Parser*. .

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. .

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. .

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. .

Rutz, Adriano, and Johannes Rainer. 2025. *CentroidR: CentroidR Provides the Infrastructure to Centroid Profile Spectra*.

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. .

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 "CentroidR" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'CentroidR: Repository to centroid profile spectra.'
version: 0.0.0.9000
abstract: CentroidR provides the infrastructure to centroid profile spectra
authors:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
- family-names: Rainer
  given-names: Johannes
  email: Johannes.Rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147
preferred-citation:
  type: manual
  title: 'CentroidR: Repository to centroid profile spectra.'
  authors:
  - family-names: Rutz
    given-names: Adriano
    email: adafede@gmail.com
    orcid: https://orcid.org/0000-0003-0443-9902
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  year: '2025'
  notes: R package, version 0.0.9000
repository: https://r-universe.dev
repository-code: https://github.com/adafede/CentroidR
url: https://adafede.github.io/CentroidR
contact:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
keywords:
- centroiding
- spectra

CodeMeta (codemeta.json)

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GitHub Events

Total

Issues event: 6
Delete event: 2
Issue comment event: 4
Public event: 1
Push event: 163
Pull request event: 3
Create event: 4

Last Year

Issues event: 6
Delete event: 2
Issue comment event: 4
Public event: 1
Push event: 163
Pull request event: 3
Create event: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 3
Total pull requests: 2
Average time to close issues: 2 minutes
Average time to close pull requests: about 6 hours
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 2

Past Year

Issues: 3
Pull requests: 2
Average time to close issues: 2 minutes
Average time to close pull requests: about 6 hours
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 2

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Dependencies

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DESCRIPTION cran

R >= 4.3.0 depends
MSnbase >= 2.28.1 imports
logger >= 0.4.0 imports
BiocManager * suggests
R.utils * suggests
knitr * suggests
spelling * suggests
testthat * suggests

inst/Dockerfile docker

bioconductor/bioconductor_docker 3.20-R-4.4.2 build