Changelog

Source: NEWS.md

MetaProViz 3.99.10 (2025-10-28)

• SummarizedExperiment support:
  • Implemention of se objects support as default input for processing(), replicate_sum(), pool_estimation(), dma(), metadata_analysis(), meta_pk(), viz_heatmap() and viz_pca()#
  • Implemention of se object output for processing(), replicate_sum() and pool_estimation()
  • Generation of example data se objects intracell_raw_se.rda and tissue_norm_se.rda in /data folder
• First candidate for Bioconductor submission

MetaProViz 3.99.1 (2025-10-08)

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

MetaProViz 3.99.0 (2025-09-30)

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

MetaProViz 3.0.3 (2025-07-16)

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

MetaProViz 3.0.2 (2025-06-13)

• Extended sample-metadata vignette
• Revamped prior knowledge documentation

MetaProViz 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

MetaProViz 2.1.7 (2025-04-01)

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

MetaProViz 2.1.6 (2025-02-28)

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

MetaProViz 2.1.5 (2025-02-21)

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

MetaProViz 2.1.4 (2025-01-15)

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

MetaProViz 2.1.3 (2024-12-20)

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

MetaProViz 2.1.2 (2024-11-04)

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

MetaProViz 2.1.1 (2024-10-24)

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

MetaProViz 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

MetaProViz 2.0.2 (2024-06-13)

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

MetaProViz 2.0.1 (2024-04-22)

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

MetaProViz 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

MetaProViz 1.0.1 (2024-01-30)

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

MetaProViz 1.0.0 (2023-11-09)

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