Files in biodev/packageDir
Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/DrugDbFunctions.R
R/InitiateDataStructures.R
R/OverlapAnalysisFunctions.R
R/PolyPhenAppend.R
R/PolyPhenProcessing_functions.R
R/SettingsObjectInterface.R
R/acc_functions.R
R/addCohortEnrichToIndividuals.R
R/biopaxToCytoscape.R
R/corsym.R
R/drugDbInterface.R
R/drug_screen_nuevo.R
R/filterMafToMutsig.R
R/generic_aberration_summary.R
R/hypergeometricPathAnalysis.R
R/installBioconductorPackages.R
R/main.R
R/main_functions.R
R/newOLA.R
R/nozzleBuilder.R
R/path_paint.R
R/pathway_functions.R
R/processOHSUseqDat.R
R/processOHSUseqDat_functions.R
R/processSomaticSeqDataWithCoverage.R
R/runShiny.R
R/save_and_load_data.R
R/somatic_mutations_processing_v8.R
R/summaryTable5.R
R/summaryTableFunctions.R
R/testAndDefaultDataScripts.R
errorLog/trying sendNetToCytoscape.txt
inst/extdata/2161541.owl
inst/extdata/Drug_Screen_test_File.txt
inst/extdata/Drug_Screen_test_File_overlap_insensitive_partial.txt
inst/extdata/MAFcolorMatches.txt
inst/extdata/Reactome.2014.04.06.12.52.27.txt
inst/extdata/Somatic_mutations_test_file_Abacavir_metabolism_enriched.maf
inst/extdata/abacavirActiveGenesEachPath.rda
inst/extdata/abacavirSettings.rda
inst/extdata/amlDrugScreenSum.rda
inst/extdata/amlSomaticSum.rda
inst/extdata/amlSymbolsUncorrected.rda
inst/extdata/basicPathInfoAbacavir.rda
inst/extdata/basicPathInfoAbacavirCoverage.rda
inst/extdata/colorMatches.txt
inst/extdata/currentPathSum.rda
inst/extdata/defOLASettings.rda
inst/extdata/defaultSummaryTable140504.rdata
inst/extdata/exampleResults.rda
inst/extdata/exampleSettings.rda
inst/extdata/gene_symbol_corrections_list.txt
inst/extdata/generalSummary.rda
inst/extdata/getDrugTargetDataTestData.rda
inst/extdata/getDrugTargetDataTestDataTrueOutput.rda
inst/extdata/hypergeometricPathEnrichmentRes.rda
inst/extdata/intTest_overlapAnalysisSlots.rda
inst/extdata/intTest_subfunPathSum.rda
inst/extdata/intTest_subsomaticPathSum.rda
inst/extdata/originalDataMatrix
inst/extdata/pathMetaData.txt
inst/extdata/pathSummaryRunnerObject.rda
inst/extdata/pgm.rda
inst/extdata/record_of_biopax_pathways.txt
inst/extdata/studyTestDatNoPathsNoSymTab.rda
inst/extdata/targetPathSum.rda
inst/extdata/test.checkForceRowNames.rda
inst/extdata/testStudySettings.rda
inst/extdata/testTarget.checkForceRowNames.rda
inst/extdata/uniqueColorPalette.txt
inst/shinyDrugSelect/server.R
inst/shinyDrugSelect/ui.R
inst/testData/abacavirActiveGenesEachPath.rda
inst/testData/amlDrugScreenSum.rda
inst/testData/amlSomaticSum.rda
inst/testData/amlSymbolsUncorrected.rda
inst/testData/basicPathInfoAbacavir.rda
inst/testData/basicPathInfoAbacavirCoverage.rda
inst/testData/currentPathSum.rda
inst/testData/defOLASettings.rda
inst/testData/exampleResults.rda
inst/testData/exampleSettings.rda
inst/testData/generalSummary.rda
inst/testData/getDrugTargetDataTestData.rda
inst/testData/getDrugTargetDataTestDataTrueOutput.rda
inst/testData/hypergeometricPathEnrichmentRes.rda
inst/testData/intTest_overlapAnalysisSlots.rda
inst/testData/intTest_subfunPathSum.rda
inst/testData/intTest_subsomaticPathSum.rda
inst/testData/originalDataMatrix
inst/testData/pgm.rda
inst/testData/studyTestDatNoPathsNoSymTab.rda
inst/testData/targetPathSum.rda
inst/testData/test.checkForceRowNames.rda
inst/testData/testStudySettings.rda
inst/testData/testTarget.checkForceRowNames.rda
inst/unitTests/DataObjectCreationScripts.R
inst/unitTests/souceAll.R
inst/unitTests/test_1.R
inst/unitTests/test_2.R
inst/unitTests/test_21.R
inst/unitTests/test_3.R
inst/unitTests/test_4.R
inst/unitTests/test_5.R
installBioconductorPackages.R
man/BangForBuck.Rd
man/DataArm-class.Rd
man/DataSummary.Rd
man/PathSummaryRunner-class.Rd
man/Path_Detail-class.Rd
man/PolyPhenFromMaf.Rd
man/SaveToHTML.Rd
man/Study-class.Rd
man/StudyMetaData-class.Rd
man/abDrugOverlapAnalysis.Rd
man/addBangForBuck.Rd
man/addCohortToIndividuals.Rd
man/addCorrections.Rd
man/addPathwayImagesWithSelection.Rd
man/addSequenceCaptureArm.Rd
man/allInteractiveMainFunction.Rd
man/armDescriptionList.Rd
man/autoRunFromSettings.Rd
man/checkFileCopyDefault.Rd
man/compareSources.Rd
man/coreOverlapAnalysis.Rd
man/correctByHgncHelper.Rd
man/corsym.Rd
man/dot-loadGraphitePaths.Rd
man/downloadHugoLookupTable.Rd
man/extractPathNames.Rd
man/getAlternateNames.Rd
man/getBasicSettings.Rd
man/getComments.Rd
man/getDefaultPaths.Rd
man/getDefaultSettings.Rd
man/getGenesFromPaths.Rd
man/getHugoSymbols.Rd
man/getHumanPathIds.Rd
man/getLoadedPathSummaryRunner.Rd
man/getNodePositionTable.Rd
man/getPathIdsToTarget.Rd
man/getPaths.Rd
man/getPathsWithGenes.Rd
man/getPathwaysRecords.Rd
man/getPublicationRefs.Rd
man/getReactomeBiopax.Rd
man/getReactomeIds.Rd
man/getStudyObject.Rd
man/getTestPGM.Rd
man/getTestPathSummaryRunner.Rd
man/getTestStudyObject.Rd
man/getTestStudySettings.Rd
man/hypergeometricPathEnrichment.Rd
man/importAllGraphite.Rd
man/initiateStudy.Rd
man/list_to_table.Rd
man/loadBasicArms.Rd
man/loadDataArm.Rd
man/loadPathSigTests.Rd
man/loadStudy.Rd
man/makeDrugSelectionWorksheet.Rd
man/nodeNamesFromLabels.Rd
man/openPGM.Rd
man/patientSummaryToNozzleReport.Rd
man/prepPathListForSave.Rd
man/printProgramState.Rd
man/runArm.Rd
man/runDrugWorksheet.Rd
man/runSomaticMutationsProcessing.Rd
man/saveDataWorkUpNotes.Rd
man/saveStudy.Rd
man/selectAndLoadSettings.Rd
man/setBorderColors.Rd
man/setCutoff.Rd
man/setNodeColors.Rd
man/settingList.Rd
man/summarize_by.Rd
man/summaryTable.Rd
man/twoHistOnePlot.Rd
man/unfactorize.Rd
man/whichPaths.Rd
packageDir.Rproj
reference_data/paths/Reactome.2014.04.06.12.52.27.txt
reference_data/paths/pathMetaData.txt
tests/run_tests.R
