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Changelog

Source: NEWS.md

mrmhub 0.9.9 (development)

This release focuses on usability, robustness, and new functions.

Highlights

  • Considerably enhanced console output and error messages: clearer, more actionable messages, up-front argument validation, and truthful processing summaries make each step easier to follow and debug.

  • Substantially improved data and metadata import: more robust sample and feature ID normalization and matching, deduplication, and stronger schema validation greatly reduce silent input errors.

  • Consistent, configurable plotting: shared appearance arguments (font sizes, colours, legend placement and sizing) with a refined house theme, now settable globally via mrmhub_set_plot_defaults().

  • Flexible figure export: the new save_plot() writes any plot_*() figure to a file at a defined physical size and format, including multi-page PDFs, and the paged plot functions gain configurable page dimensions.

  • MS1 and MS2 (MRM) isotope interference correction: a full correction engine for both precursor (MS1) and transition-level (MRM) isotopic interferences, with MRM patterns based on the LICAR method (Gao et al., Anal. Chem., 2021).

  • New batch-correction methods (experimental): empirical-Bayes ComBat (correct_batch_combat(), Johnson et al. 2007) and SERRF random-forest normalization (correct_batch_serrf(), Fan et al. 2019), complementing the existing correct_batch_centering().

  • Export to SummarizedExperiment and LipidomicsExperiment: results convert directly to Bioconductor SummarizedExperiment and lipidr LipidomicsExperiment objects for downstream analysis.

  • Save, share, and reload complete experiments: save_dataset_rds() and read_dataset_rds() serialize a whole MRMhubExperiment to a single, self-contained .rds file, making complete datasets easy to archive and share; a content hash is embedded on save and verified on load.

  • Further new features: mzTab-M import and export, and a status dashboard (mrmhub_status()) with compact object printing for a quick overview.

  • Improved robustness, speed, and stability: better handling of missing values and analytical-sequence gaps, faster QC-metric computation, and many bug fixes based on user feedback.

  • Fully revised documentation: a rewritten, task-oriented site with tutorials, manual, and recipes.

mrmhub 0.9.2

Initial public version.