Changes in version 0.99.0                        

New features

  - Added normalize_mean() and full pipeline builder supporting TIC,
    PQN, Quantile, VSN, Median, Mean, Log2, Log10, Sqrt, None
  - Added get_normalization_descriptions() for UI help text
  - Shiny app: Select All / Deselect All buttons on every checkbox group
  - Shiny app: group-coloured normalization comparison plots
  - Shiny app: full plot history tracked across the session for complete
    reports
  - Shiny app: samples sorted by group in Lipid Expression plots
  - Shiny app: descriptive, timestamped download filenames for all plots

Bug fixes

  - create_pca_plot_with_ellipses(): fixed duplicate legend keys when
    ellipses are drawn (fill + color legends now merged into one)
  - create_lipid_expression_barplot(): samples now sorted by group, not
    by sample name
  - Excel export: worksheet names truncated to Excel's 31-character
    limit
  - Normalization help text modal and ellipse help modal now display
    correctly
  - perform_plsda(): replaced cat() with message() (Bioconductor
    requirement)
  - perform_enrichment_analysis(): replaced cat() with message()

Notes

  - Quantile normalization producing near-identical boxplots is expected
    and correct behaviour; inline documentation and UI now make this
    explicit
  - Median and Mean normalization can look similar on symmetric
    (log-normal) lipidomics data; on skewed data they differ — this is
    also expected