Data

Tools

Indexes

Applications

Experiments

Open Source Science

maldipickr

Dereplicate And Cherry-pick Mass Spectrometry Spectra

https://github.com/clavellab/maldipickr

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 7 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary

Keywords

cherry-pick dereplication maldi-tof-ms r r-packages rstats
Last synced: 7 months ago · JSON representation

Repository

Dereplicate And Cherry-pick Mass Spectrometry Spectra

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 4
  • Releases: 11
Topics
cherry-pick dereplication maldi-tof-ms r r-packages rstats
Created about 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Zenodo

README.md

maldipickr maldipickr website

Project Status: Active – The project has reached a stable, usable state and is being actively developed. CRAN status CRAN checks R-CMD-check codecov DOI <!-- badges: end -->

  • You are using the MALDI-TOF[^1] Biotyper to identify bacterial isolates
  • You want to select representative isolates for further experiments
  • You need fast and automated selection decisions that you can retrace

{maldipickr} provides documented and tested R functions that will help you dereplicate MALDI-TOF data and cherry-pick representative spectra of microbial isolates.

Check out the graphical overview. {maldipickr} can use two approaches: from taxonomic identification reports (left) or from spectra data (right). Click on the thumbnail for a bigger version.

Thumbnail of maldipickr graphical overview

Installation

{maldipickr} is available on the CRAN and on GitHub.

To install the latest CRAN release, use the following command in R:

r install.packages("maldipickr")

Or if you are using {renv}, use:

r renv::install("maldipickr")

To install the development version, use the following command in R:

``` r remotes::installgithub("ClavelLab/maldipickr", buildvignettes = TRUE)

or with renv::install("ClavelLab/maldipickr")

```

Usage

Start off with the Introduction to maldipickr for a quickstart. Otherwise, the comprehensive vignettes will walk you through the package functions and showcase how to:

  1. Import spectra data and identification reports from Bruker MALDI Biotyper into R.
  2. Process, dereplicate and cherry-pick representative spectra, from simple to complex design.

Troubleshoot and Contribute

Troubleshoot If something unexpected happened when using this package, please first search the current open or closed issues to look for similar problems. If you are the first, you are more than welcome to open a new issue using the “Bug report” template with a minimal reprex.

Contribute All contributions are welcome and the CONTRIBUTING.md documents how to participate. Please note that the {maldipickr} package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Credits

Acknowledgements This R package is developed for spectra data generated by the Bruker MALDI Biotyper device. The {maldipickr} package is built from a suite of Rmarkdown files using the {fusen} package by Rochette S (2023). It relies on:

  1. the {MALDIquant} package from Gibb & Strimmer (2012) for spectra functions
  2. the work of Strejcek et al. (2018) for the dereplication procedure.

Disclaimer The developers of this package are part of the Clavel Lab and are not affiliated with the company Bruker, therefore this package is independent of the company and is distributed under the GPL-3.0 License. The hexagonal logo was created by Charlie Pauvert and uses the Atkinson Hyperlegible font font and a color palette generated at coolors.co.

References

[^1]: Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF)

Owner

  • Name: The Clavel lab
  • Login: ClavelLab
  • Kind: organization
  • Location: Germany

This is the official GitHub account for the research group of Prof. Thomas Clavel.

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 2
  • Push event: 2
Last Year
  • Issues event: 1
  • Issue comment event: 2
  • Push event: 2

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 260
  • Total Committers: 1
  • Avg Commits per committer: 260.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 84
  • Committers: 1
  • Avg Commits per committer: 84.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
cpauvert c****t 260

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 47
  • Total pull requests: 4
  • Average time to close issues: 28 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.64
  • Average comments per pull request: 1.75
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: 5 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cpauvert (40)
  • sarah-lital (1)
Pull Request Authors
  • cpauvert (6)
Top Labels
Issue Labels
enhancement (11) documentation (8) bug (5) good first issue (1) invalid (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 222 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: maldipickr

Dereplicate and Cherry-Pick Mass Spectrometry Spectra

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 222 Last month
Rankings
Dependent packages count: 28.2%
Forks count: 28.2%
Stargazers count: 31.2%
Dependent repos count: 36.7%
Average: 42.4%
Downloads: 87.9%
Maintainers (1)
cpauvert@ukaachen.de
Last synced: 8 months ago

Dependencies

.github/workflows/R-CMD-check.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/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/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • codecov/codecov-action v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • MALDIquant * imports
  • dplyr * imports
  • igraph * imports
  • magrittr * imports
  • readBrukerFlexData * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidygraph * imports
  • tidyr * imports
  • tidyselect * imports
  • tools * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
dev/Dockerfile docker
  • rocker/tidyverse 4.3 build