├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── coverage.yaml │ ├── lint.yaml │ ├── pr-commands.yaml │ └── test.yaml ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── enrichment_functions.R ├── feature_processing.R ├── metabolome.R ├── proteome.R ├── transcriptome.R └── utility_functions.R ├── README.md ├── data ├── metabolome.rda ├── proteome.rda └── transcriptome.rda ├── inst ├── CITATION └── NEWS.Rd ├── man ├── archiveDir.Rd ├── archivePath.Rd ├── combinePvalues.Rd ├── extractPvalues.Rd ├── getFeatures.Rd ├── getGeneMapping.Rd ├── getIDMappingDatabase.Rd ├── getMappedFeatures.Rd ├── getMetaboliteIDformats.Rd ├── getMetaboliteMapping.Rd ├── getMultiOmicsFeatures.Rd ├── getOrganisms.Rd ├── initOmicsDataStructure.Rd ├── loadLocal.Rd ├── mapIDType.Rd ├── metabolome.Rd ├── multiGSEA.Rd ├── proteome.Rd ├── rankFeatures.Rd ├── rename_duplicates.Rd └── transcriptome.Rd ├── tests ├── testthat.R └── testthat │ ├── test_combinePvalues.R │ ├── test_pathway_enrichment.R │ 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