Package: maldipickr 1.3.2
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:
maldipickr_1.3.2.tar.gz
maldipickr_1.3.2.zip(r-4.5)maldipickr_1.3.2.zip(r-4.4)maldipickr_1.3.2.zip(r-4.3)
maldipickr_1.3.2.tgz(r-4.4-any)maldipickr_1.3.2.tgz(r-4.3-any)
maldipickr_1.3.2.tar.gz(r-4.5-noble)maldipickr_1.3.2.tar.gz(r-4.4-noble)
maldipickr_1.3.2.tgz(r-4.4-emscripten)maldipickr_1.3.2.tgz(r-4.3-emscripten)
maldipickr.pdf |maldipickr.html✨
maldipickr/json (API)
NEWS
| # 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
cherry-pickdereplicationmaldi-tof-ms
Last updated 5 days agofrom:b91eb12fd4. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | OK | Sep 13 2024 |
| R-4.5-linux | OK | Sep 13 2024 |
| R-4.4-win | OK | Sep 13 2024 |
| R-4.4-mac | OK | Sep 13 2024 |
| R-4.3-win | OK | Sep 13 2024 |
| R-4.3-mac | OK | Sep 13 2024 |
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:clicpp11dplyrfansigenericsgluelifecyclemagrittrMALDIquantpillarpkgconfigpurrrR6readBrukerFlexDatarlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Dereplicate Bruker MALDI Biotyper spectra
Rendered fromdereplicate-bruker-maldi-biotyper-spectra.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-05-06
Started: 2023-03-23
Import data from Bruker MALDI Biotyper
Rendered fromimport-data-from-bruker-maldi-biotyper.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2023-09-05
Started: 2023-03-10
maldipickr
Rendered frommaldipickr.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-09-11
Started: 2024-09-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evaluate the spectra regularities | check_spectra |
| Delineate clusters from taxonomic identifications | delineate_with_identification |
| Delineate clusters from a similarity matrix | delineate_with_similarity |
| Aggregate spectra quality-check statistics | gather_spectra_stats |
| Extract spectra names and check for uniqueness | get_spectra_names |
| Importing spectra from the Bruker MALDI Biotyper device | import_biotyper_spectra |
| Import clusters results generated by SPeDE | import_spede_clusters |
| Identify the wells on the plate's edge | is_well_on_edge |
| Merge multiple processed spectra and peaks | merge_processed_spectra |
| Cherry-pick Bruker MALDI Biotyper spectra | pick_spectra |
| Process Bruker MALDI Biotyper spectra _à la_ Strejcek et al. (2018) | process_spectra |
| Importing Bruker MALDI Biotyper CSV report | read_biotyper_report |
| Importing a list of Bruker MALDI Biotyper CSV reports | read_many_biotyper_reports |
| Remove (raw or processed) spectra | remove_spectra |
| Set a reference spectrum for each cluster | set_reference_spectra |
