Installation

pip install maldiamrkit

Optional: Batch Correction & UMAP

For multi-site batch effect correction with combatlearn and UMAP-based exploratory plots:

pip install maldiamrkit[batch]

This installs combatlearn for ComBat-based batch correction and umap-learn for UMAP dimensionality reduction.

See the combatlearn documentation for usage examples. Reference:

Rocchi, E., Nicitra, E., Calvo, M. et al. Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy. BMC Microbiol (2026). doi:10.1186/s12866-025-04657-2

Development Installation

git clone https://github.com/EttoreRocchi/MaldiAMRKit.git
cd MaldiAMRKit
pip install -e .[dev]