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https://github.com/clavellab/maldipickr
Dereplicate And Cherry-pick Mass Spectrometry Spectra
https://github.com/clavellab/maldipickr
cherry-pick dereplication maldi-tof-ms r r-packages rstats
Last synced: 2 months ago
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Dereplicate And Cherry-pick Mass Spectrometry Spectra
- Host: GitHub
- URL: https://github.com/clavellab/maldipickr
- Owner: ClavelLab
- License: gpl-3.0
- Created: 2023-03-13T09:35:56.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-13T12:09:10.000Z (3 months ago)
- Last Synced: 2024-10-12T18:00:13.518Z (2 months ago)
- Topics: cherry-pick, dereplication, maldi-tof-ms, r, r-packages, rstats
- Language: R
- Homepage: https://clavellab.github.io/maldipickr/
- Size: 8.63 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# maldipickr 
[](https://www.repostatus.org/#active)
[](https://CRAN.R-project.org/package=maldipickr)
[](https://cran.r-project.org/web/checks/check_results_maldipickr.html)
[](https://github.com/ClavelLab/maldipickr/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/github/ClavelLab/maldipickr)
[](https://doi.org/10.5281/zenodo.13759021)
- 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.
>
> 
## Installation
`{maldipickr}` is available on the
[CRAN](https://cran.r-project.org/package=maldipickr) and on
[GitHub](https://github.com/ClavelLab/maldipickr).
To install the latest CRAN release, use the following command in R:
``` r
install.packages("maldipickr")
```
Or if you are using [`{renv}`](https://cran.r-project.org/package=renv),
use:
``` r
renv::install("maldipickr")
```
To install the development version, use the following command in R:
``` r
remotes::install_github("ClavelLab/maldipickr", build_vignettes = TRUE)
# or with renv::install("ClavelLab/maldipickr")
```
## Usage
Start off with the [Introduction to
maldipickr](https://clavellab.github.io/maldipickr/articles/maldipickr.html)
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](https://clavellab.github.io/maldipickr/articles/import-data-from-bruker-maldi-biotyper.html).
2. [Process, dereplicate and cherry-pick representative spectra, from
simple to complex
design](https://clavellab.github.io/maldipickr/articles/dereplicate-bruker-maldi-biotyper-spectra.html).
## Troubleshoot and Contribute
**Troubleshoot** If something unexpected happened when using this
package, please first search the [current open or closed
issues](https://github.com/ClavelLab/maldipickr/issues?q=is%3Aissue++)
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](https://www.tidyverse.org/help/#reprex).
**Contribute** All contributions are welcome and the
[`CONTRIBUTING.md`](https://clavellab.github.io/maldipickr/CONTRIBUTING.html)
documents how to participate. Please note that the
[`{maldipickr}`](https://github.com/ClavelLab/maldipickr) package is
released with a [Contributor Code of
Conduct](https://clavellab.github.io/maldipickr/CODE_OF_CONDUCT.html).
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}`](https://github.com/ClavelLab/maldipickr) package is
built from a suite of Rmarkdown files using the
[`{fusen}`](https://thinkr-open.github.io/fusen/) package by Rochette S
(2023). It relies on:
1. the [`{MALDIquant}`](https://cran.r-project.org/package=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](https://www.ukaachen.de/kliniken-institute/institut-fuer-medizinische-mikrobiologie/forschung/ag-clavel/)
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](https://clavellab.github.io/maldipickr/LICENSE.html). The
hexagonal logo was created by Charlie Pauvert and uses the [Atkinson
Hyperlegible
font](https://fonts.google.com/specimen/Atkinson+Hyperlegible/about)
font and a color palette generated at
[coolors.co](https://coolors.co/cf5c36-f0f0c9-555358).
## References
- Gibb S & Strimmer K (2012). “MALDIquant: a versatile R package for the
analysis of mass spectrometry data”. *Bioinformatics* 28, 2270-2271.
.
- Rochette S (2023). “fusen: Build a Package from Rmarkdown Files”.
,
.
- Strejcek M, Smrhova T, Junkova P & Uhlik O (2018). “Whole-Cell
MALDI-TOF MS versus 16S rRNA Gene Analysis for Identification and
Dereplication of Recurrent Bacterial Isolates.” *Frontiers in
Microbiology* 9 .
[^1]: Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight
(MALDI-TOF)
