├── .Rbuildignore ├── .bumpversion.cfg ├── .github └── workflows │ ├── build-check.yaml │ └── pkgdown-github-pages.yaml ├── .gitignore ├── CLAUDE.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── DifferentialMetaboliteAnalysis.R ├── GetPriorKnowledge.R ├── HelperChecks.R ├── HelperLog.R ├── HelperMisc.R ├── HelperOptions.R ├── HelperPlots.R ├── HelperSave.R ├── HelperSummarizedExperiment.R ├── MetaDataAnalysis.R ├── MetaProViz.R ├── MetaboliteClusteringAnalysis.R ├── OverRepresentationAnalysis.R ├── Processing.R ├── RefactorPriorKnoweldge.R ├── ToyData.R ├── VizHeatmap.R ├── VizPCA.R ├── VizStackedbar.R ├── VizSuperplots.R ├── VizUpset.R ├── VizVolcano.R ├── aaa_MetaProViz_Env.R ├── enricher_internal.R ├── pipe.R └── zzz.R ├── README.md ├── data ├── alanine_pathways.rda ├── biocrates_features.rda ├── cellular_meta.rda ├── equivalent_features.rda ├── gaude_pathways.rda ├── hallmarks.rda ├── intracell_dma.rda ├── intracell_raw.rda ├── intracell_raw_se.rda ├── mca_core_rules.rda ├── mca_twocond_rules.rda ├── medium_raw.rda ├── tissue_dma.rda ├── tissue_dma_old.rda ├── tissue_dma_young.rda ├── tissue_meta.rda ├── tissue_norm.rda ├── tissue_norm_se.rda ├── tissue_tvn_proteomics.rda └── tissue_tvn_rnaseq.rda ├── inst ├── CITATION └── scripts │ └── readme-figure.R ├── man ├── MetaProViz.Rd ├── alanine_pathways.Rd ├── biocrates_features.Rd ├── cellular_meta.Rd ├── checkmatch_pk_to_data.Rd ├── cluster_ora.Rd ├── compare_pk.Rd ├── count_id.Rd ├── dma.Rd ├── equivalent_features.Rd ├── equivalent_id.Rd ├── gaude_pathways.Rd ├── hallmarks.Rd ├── intracell_dma.Rd ├── intracell_raw.Rd ├── intracell_raw_se.Rd ├── make_gene_metab_set.Rd ├── mapping_ambiguity.Rd ├── mca_2cond.Rd ├── mca_core.Rd ├── mca_core_rules.Rd ├── mca_twocond_rules.Rd ├── medium_raw.Rd ├── meta_pk.Rd ├── metadata_analysis.Rd ├── metaproviz_config_path.Rd ├── metaproviz_load_config.Rd ├── metaproviz_log.Rd ├── metaproviz_logfile.Rd ├── metaproviz_reset_config.Rd ├── metaproviz_save_config.Rd ├── metaproviz_set_loglevel.Rd ├── metsigdb_chemicalclass.Rd ├── metsigdb_kegg.Rd ├── metsigdb_metalinks.Rd ├── pool_estimation.Rd ├── processing.Rd ├── reexports.Rd ├── replicate_sum.Rd ├── standard_ora.Rd ├── tissue_dma.Rd ├── tissue_dma_old.Rd ├── tissue_dma_young.Rd ├── tissue_meta.Rd ├── tissue_norm.Rd ├── tissue_norm_se.Rd ├── tissue_tvn_proteomics.Rd ├── tissue_tvn_rnaseq.Rd ├── translate_id.Rd ├── viz_heatmap.Rd ├── viz_pca.Rd ├── viz_superplot.Rd └── viz_volcano.Rd ├── pkgdown ├── _pkgdown.yml └── extra.css ├── tests ├── testthat.R └── testthat │ ├── test-check_param.R │ ├── test-checkmatch_pk_to_data.R │ └── test-cluster_ora.R └── vignettes ├── .gitignore ├── Fig.1.png ├── Fig.2.png ├── Fig.3.png ├── Hexagon_MetaProViz.png ├── bibliography.bib ├── pkgdown ├── bibliography.bib ├── core-metabolomics.Rmd ├── prior-knowledge.Rmd ├── prior-knowledge.Rmd_compare-pk-2.svg ├── prior-knowledge.Rmd_compare-pk-3.svg ├── prior-knowledge.Rmd_compare-pk.svg ├── 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