Package: maldipickr 1.3.3

Charlie Pauvert

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.

Authors:Charlie Pauvert [aut, cre, cph], David Wylensek [ctb], Selina Nüchtern [ctb], Thomas Clavel [ctb, fnd, cph]

maldipickr_1.3.3.tar.gz
maldipickr_1.3.3.zip(r-4.7-any)maldipickr_1.3.3.zip(r-4.6-any)maldipickr_1.3.3.zip(r-4.5-any)
maldipickr_1.3.3.tgz(r-4.6-any)maldipickr_1.3.3.tgz(r-4.5-any)
maldipickr_1.3.3.tar.gz(r-4.7-any)maldipickr_1.3.3.tar.gz(r-4.6-any)
maldipickr_1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
maldipickr/json (API)

# Install 'maldipickr' in R:
install.packages('maldipickr', repos = c('https://clavellab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/clavellab/maldipickr/issues

Pkgdown/docs site:https://clavellab.github.io

On CRAN:

Conda:

cherry-pickdereplicationmaldi-tof-ms

5.17 score 3 stars 11 scripts 433 downloads 16 exports 22 dependencies

Last updated from:0560a8f825. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK142
source / vignettesOK216
linux-releaseOK130
macos-releaseOK202
macos-oldrelOK214
windows-develOK91
windows-releaseOK96
windows-oldrelOK85
wasm-releaseOK133

Exports:%>%check_spectradelineate_with_identificationdelineate_with_similaritygather_spectra_statsget_spectra_namesimport_biotyper_spectraimport_spede_clustersis_well_on_edgemerge_processed_spectrapick_spectraprocess_spectraread_biotyper_reportread_many_biotyper_reportsremove_spectraset_reference_spectra

Dependencies:clicpp11dplyrgenericsgluelifecyclemagrittrMALDIquantpillarpkgconfigpurrrR6readBrukerFlexDatarlangstringistringrtibbletidyrtidyselectutf8vctrswithr

maldipickr
Quickstart | Using taxonomic identification report | Get example data | Delineate clusters and cherry-pick | Using spectra data | Session information
Rendered frommaldipickr.Rmdusingknitr::rmarkdown

Last update: 2024-09-11
Started: 2024-09-11

Dereplicate Bruker MALDI Biotyper spectra
Process Bruker MALDI Biotyper spectra | Process from raw spectra to peak filtering | Merge multiple processed spectra | Compute a similarity matrix between all processed spectra (not included) | Delineate clusters of spectra | From a similarity matrix | Similarity to clusters | Set a reference spectrum for each cluster | From taxonomic identifications | Import clusters results generated by SPeDE | Cherry-pick Bruker MALDI Biotyper spectra | References
Rendered fromdereplicate-bruker-maldi-biotyper-spectra.Rmdusingknitr::rmarkdown

Last update: 2024-05-06
Started: 2023-03-23

Import data from Bruker MALDI Biotyper
Importing generated reports from the Bruker MALDI Biotyper device | Importing a single report | Importing multiple reports | Importing spectra from the Bruker MALDI Biotyper device | Importing multiple spectra from a directory hierarchy | Evaluate the quality of the spectra
Rendered fromimport-data-from-bruker-maldi-biotyper.Rmdusingknitr::rmarkdown

Last update: 2023-09-05
Started: 2023-03-10