- Added a unified table workflow with sample/feature metadata
validation, batch-aware blank filtering, missing-value handling,
QC-RLSC/PQN normalization, and processing records.
- Added two-group comparisons using Welch or Wilcoxon tests with
Benjamini-Hochberg adjusted p-values.
- Added self-contained HTML QC reports and complete result bundles
with original inputs, processed tables, feature/sample metadata, QC
summaries, and settings.
- MS1 annotation now searches CEU Mass Mediator through the optional
cmmr package. The legacy annotation database and external data-release
downloader were removed.
- Retained SCIEX/Qtrap processing, targeted calibration, robust sample
QC, PCA, heatmaps, LC-MS feature plots, spectrum plotting, and MSP
writing.
- Removed the legacy OmicsData S4/synthetic-data system, generic
predictive modeling, feature selection, graph/enrichment displays,
raw-file MS/MS inspection/conversion, and incomplete or duplicate app
screens. These are intentional breaking API changes from CRAN version
1.1.7.
- Reduced required external dependencies and replaced the app wrapper
with the standard Shiny launcher. Excel import and specialized exports
are optional.
- Updated package authorship. Amrita Cheema is the designated
maintainer at metabolomics@georgetown.edu.
- Added the hex logo and horizontal workflow figure. Standalone QC
reports omit personal credits while preserving author metadata in
exported settings.