NEWS

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omicsTools 2.0.0

• 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 [email protected].
• Added the hex logo and horizontal workflow figure. Standalone QC reports omit personal credits while preserving author metadata in exported settings.