rformassspectrometry/Metabonaut: v1.4.0

Metabonaut v1.4.0 🧑‍🚀 Welcome to the latest release of Metabonaut! This version introduces significant workflow expansions, including robust new tools for quality control and feature selection, and updates our core compatibility to the latest Bioconductor ecosystem. 🚀 What's New in v1.4.0? 🧪 New Vignettes & Workflow Enhancements Quality Control and Feature Selection with notame: We've added a dedicated vignette for the notame package. This provides a powerful alternative for normalization and feature selection, ensuring your metabolomics data is clean and statistically sound. GNPS Export & Peak-Picking: The main workflow now includes integrated steps for GNPS export and a comprehensive summary of peak-picking results. Enhanced Dataset Investigation: New visual examples have been added to the "Dataset Investigation" vignette, including foreground/background comparisons and a visual guide to the effect of filterPeaksRanges. Expanded Documentation: Added detailed descriptions for parameters like firstBaselineCheck to help users fine-tune their preprocessing. ⚙️ Technical Updates & Stability Bioconductor 3.22: Metabonaut is now fully updated for BioC 3.22. Bug Fixes: Fixed subsetting issues for Control samples during MS2 annotation. Dependency Management: Improved workflow stability by resolving missing library dependencies (e.g., knitr). Reference Updates: Updated the xcms references to reflect the latest standards in the field. 📚 Updated Vignette Overview Complete End-to-End LC-MS/MS Analysis: From raw data preprocessing to final metabolite annotation. Dataset Investigation: Critical first steps to examine your data and prevent downstream troubleshooting. Seamless Alignment: Integrating new datasets with existing preprocessed data using flexible alignment. QC & Feature Selection (Using notame) [NEW]: Robust normalization and cleaning of your metabolomics features. LC-MS/MS Data Annotation (R & Python): Leveraging the SpectriPy package to combine the best of both languages. Large Scale Processing: Practical guide to handling >4,000 files on a standard computer using xcms. 🤝 Community & Contributions A huge thank you to our contributors for this release! New Contributors: @kozo2 made their first contribution in PR #37 @vsuksi made their first contribution in PR #57 Full Changelog: [v1.2.0...v1.4.0](https://github.com/rformassspectrometry/Metabonaut/compare/v1.2.0...v1.4.0) Acknowledgment Funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and unifying blood metabolic analysis networks.