├── .DS_Store ├── .Rbuildignore ├── .appveyor.yml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── connectToRaMP.R ├── processNewRamp.R ├── rampFastQueryTab2.R ├── rampFastQueryTab3.R ├── rampFastQueryTab4.R ├── rampFastQueryTab5.R ├── rampQueryHelper.R ├── runRaMP.R ├── sysdata.rda └── writingFunctions.R ├── README.md ├── RaMP.Rproj ├── inst ├── extdata │ ├── .DS_Store │ ├── analytes_overlap_matrix.RData │ ├── gene.metab.IntLIM.res.RData │ ├── gene.metab.T.test.res.RData │ ├── genes_overlap_matrix.RData │ ├── genes_overlap_matrix180430.RData │ ├── metabolites_overlap_matrix.RData │ ├── metabolites_overlap_matrix180430.RData │ └── ramp180302.sql.gz └── shinyApp │ ├── FisherTestDataGenes.csv │ ├── FisherTestDataMetabolites.csv │ ├── analyte.csv │ ├── biofluid.csv │ ├── dataFisherTest.csv │ ├── db.properties.template │ ├── global.R │ ├── pathway.csv │ ├── server.R │ ├── server │ ├── tab2.R │ ├── tab3.R │ ├── tab4.R │ └── tab5.R │ ├── source.csv │ ├── ui.R │ ├── ui │ ├── header.R │ ├── side.R │ ├── uitab2.R │ ├── uitab3.R │ ├── uitab4.R │ ├── uitab5.R │ └── uitababout.R │ └── www │ ├── Rplots.pdf │ ├── fourVennCompound.jpg │ ├── fourVennGene.jpg │ ├── google_analytics.html │ ├── img1.png │ ├── jquery-1.11.2.min.js │ ├── rampstyle.css │ └── threeVennApoptosis.jpg ├── install.R ├── man ├── FilterFishersResults.Rd ├── compute_overlap_matrix.Rd ├── connectToRaMP.Rd ├── findAnalyteHasPathway.Rd ├── findCluster.Rd ├── getAnalyteFromPathway.Rd ├── getMetaFromOnto.Rd ├── getOntoFromMeta.Rd ├── getPathwayFromAnalyte.Rd ├── plotCataNetwork.Rd ├── processData.Rd ├── rampFastCata.Rd ├── rampFastPathFromSource.Rd ├── rampFileOfAnalytes_tab4.Rd ├── rampFindSourceFromId.Rd ├── rampFindSourceRampId.Rd ├── rampFindSynonymFromSynonym.Rd ├── runCombinedFisherTest.Rd ├── runFisherTest.Rd ├── runRaMPapp.Rd ├── sysdataObject.Rd ├── updateOverlapMatrices.Rd ├── updateOverlapMatrix.Rd ├── writePathwaysToCSV.Rd └── write_FishersResults.Rd └── runtime.txt /.DS_Store: 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