maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation
Abstract
Motivation: Microbiologists use MALDI-TOF for fast and cheap identification of microbial isolates. However, most standard procedures rely on a commercial database. Bioinformatic tools to dereplicate MALDI-TOF spectra have been developed, but an open and resource-efficient tool to reduce the redundancy of microbial isolates is lacking. Here we develop "maldipickr" for de novo-clustering of MALDI-TOF spectra to dereplicate and select isolates, and thereby facilitate large-scale cultivation projects. Availability and implementation: The R package "maldipickr" is available through CRAN at https://doi.org/10.32614/CRAN.package.maldipickr along extensive documentation at https://clavellab.github.io/maldipickr.
Fields of Study & Subjects
Bacterial Identification and Susceptibility Testing
Cell Image Analysis Techniques
Genomics and Phylogenetic Studies
Publication details
- Journal / source
- Bioinformatics Advances
- Publisher
- Oxford University Press (OUP)
- Volume
- 6
- Issue
- 1
- Pages
- vbag171–vbag171
- Publication date
- 1 January 2026
- Language
- EN