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maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

Convenient wrapper functions for the analysis of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra data in order to select only representative spectra (also called cherry-pick). The package covers the preprocessing and dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik (2018) <doi:10.3389/fmicb.2018.01294>) needed to cluster MALDI-TOF spectra before the final cherry-picking step. It enables the easy exclusion of spectra and/or clusters to accommodate complex cherry-picking strategies. Alternatively, cherry-picking using taxonomic identification MALDI-TOF data is made easy with functions to import inconsistently formatted reports.

Version: 1.3.1
Depends: R (≥ 3.2.0)
Imports: dplyr, lifecycle, magrittr, MALDIquant, readBrukerFlexData, rlang, stats, tibble, tidyr, tidyselect, tools, utils
Suggests: coop, knitr, rmarkdown, spelling, testthat
Published: 2024-09-12
DOI: 10.32614/CRAN.package.maldipickr
Author: Charlie Pauvert ORCID iD [aut, cre, cph], David Wylensek ORCID iD [ctb], Selina Nüchtern [ctb], Thomas Clavel ORCID iD [ctb, fnd, cph]
Maintainer: Charlie Pauvert <cpauvert at ukaachen.de>
BugReports: https://github.com/ClavelLab/maldipickr/issues
License: GPL (≥ 3)
URL: https://github.com/ClavelLab/maldipickr, https://clavellab.github.io/maldipickr/
NeedsCompilation: no
Language: en-US
Citation: maldipickr citation info
Materials: README NEWS
CRAN checks: maldipickr results

Documentation:

Reference manual: maldipickr.pdf
Vignettes: dereplicate-bruker-maldi-biotyper-spectra (source, R code)
import-data-from-bruker-maldi-biotyper (source, R code)
maldipickr (source, R code)

Downloads:

Package source: maldipickr_1.3.1.tar.gz
Windows binaries: r-devel: maldipickr_1.3.1.zip, r-release: maldipickr_1.3.1.zip, r-oldrel: maldipickr_1.3.1.zip
macOS binaries: r-release (arm64): maldipickr_1.3.1.tgz, r-oldrel (arm64): maldipickr_1.3.1.tgz, r-release (x86_64): maldipickr_1.3.1.tgz, r-oldrel (x86_64): maldipickr_1.3.1.tgz
Old sources: maldipickr archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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