Changes in version 3.99.40 (2026-02-18)                 

  - New cluster_pk() function for clustering prior knowledge terms
  - New viz_graph() function for network graph visualization
  - SummarizedExperiment support extended to viz_superplot()
  - Bug fixes in processing(), viz_volcano(), dma(), and ORA functions
  - NA handling improvements for correlation analysis
  - License changed from GPLv3 to BSD 3-clause
  - Code quality improvements for Bioconductor compliance
  - Added ggraph dependency
  - Updated documentation and argument descriptions

                Changes in version 3.99.10 (2025-10-28)                 

  - SummarizedExperiment support as default input and output
  - First candidate for Bioconductor submission

                 Changes in version 3.99.1 (2025-10-08)                 

  - Fixed Bioconductor timeout issues
  - Code refactoring to meet Bioconductor quality standards

                 Changes in version 3.99.0 (2025-09-30)                 

  - General refactoring to meet Bioconductor checks
  - RCMD check improvements
  - Updated GitHub actions workflows

                 Changes in version 3.0.3 (2025-07-16)                  

  - Enhanced processing() function to accept any column name
  - Fixed bug in missing value imputation
  - Updated README links

                 Changes in version 3.0.2 (2025-06-13)                  

  - Extended sample-metadata vignette
  - Revamped prior knowledge documentation

                 Changes in version 3.0.1 (2025-05-22)                  

  - Major version increase with API overhaul
  - Renamed parameters and functions following snake_case conventions
    for improved consistency
  - Updated all documentation to reflect new naming conventions

                 Changes in version 2.1.7 (2025-04-01)                  

  - Extended prior knowledge vignette
  - Enhanced documentation
  - Added new example datasets

                 Changes in version 2.1.6 (2025-02-28)                  

  - Bug fix in DMA() function for non-CoRe datasets

                 Changes in version 2.1.5 (2025-02-21)                  

  - User-requested bug fixes
  - Added new CheckIDMatch() function

                 Changes in version 2.1.4 (2025-01-15)                  

  - Added chemical class enrichment functionality
  - New proteomics and transcriptomics example datasets

                 Changes in version 2.1.3 (2024-12-20)                  

  - Updated parameter descriptions
  - Improved translateID() function
  - Fixed PreProcessing() issues

                 Changes in version 2.1.2 (2024-11-04)                  

  - Added unit tests
  - Updated parameter descriptions and dependencies
  - Fixed TIC=FALSE error in preprocessing

                 Changes in version 2.1.1 (2024-10-24)                  

  - Updated dependencies
  - Improved Processing() function with bug fixes
  - Enhanced figure formatting options
  - Introduced GitHub actions

                 Changes in version 2.1.0 (2024-10-02)                  

  - Updated visualization helper functions for ggplot2 compatibility
  - Added metadata analysis features with new vignette
  - Expanded prior knowledge options
  - Added ID translation functionality

                 Changes in version 2.0.2 (2024-06-13)                  

  - Introduced VizSuperplot() function
  - Added vignette examples for superplots
  - Modified VizPCA() and VizVolcano() helper functions

                 Changes in version 2.0.1 (2024-04-22)                  

  - PoolEstimation() now saves PCA plots
  - Enhanced PreProcessing() for CoRe data handling
  - Improved blank sample processing

                 Changes in version 2.0.0 (2024-04-18)                  

  - Parameter syntax redesign for more intuitive usage
  - Implemented helper functions for data validation
  - Added figure management functions
  - Added HMDB IDs to metadata

                 Changes in version 1.0.1 (2024-01-30)                  

  - Initial release adjustments
  - Enabled alternate column names for conditions in sample settings

                 Changes in version 1.0.0 (2023-11-09)                  

  - First stable release
  - Core metabolomics preprocessing functionality
  - Differential metabolite analysis
  - Comprehensive visualization tools
  - Prior knowledge integration