API for biodev/packageDir
Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.
| Global functions | |
|---|---|
| .loadGraphitePaths | Man page Source code |
| AlterVariantClassification | Source code |
| AutoSavePlot | Source code |
| BangForBuck | Man page Source code |
| CheckConvertDataType | Source code |
| CheckIntegratePolyPhen | Source code |
| CheckPatientOverlap | Source code |
| DataArm-class | Man page |
| DataSummary | Man page Source code |
| Data_work_up_notes_nozzle | Source code |
| DrugMultiScoreReduce | Source code |
| DrugScreenFromStackedFormat | Source code |
| FilterDuplicates | Source code |
| FilterVariantType | Source code |
| FilterdbSNP | Source code |
| GSEAImport | Source code |
| GenesInPaths | Source code |
| MafDataKeys | Source code |
| PGMFromVector | Source code |
| PGMFromVectorWithSelection | Source code |
| PPMultiMapRedux | Source code |
| PathSummaryRunner | Man page |
| PathSummaryRunner-class | Man page |
| Path_Detail | Man page |
| Path_Detail-class | Man page |
| Paths | Source code Source code |
| PolyPhenFromMaf | Man page Source code |
| PrintOpeningMessage | Source code |
| RunDrugScreen | Source code |
| RunGenericEnrichment | Source code |
| RunGenericEnrichment_main | Source code |
| RunOverlapAnalysis | Source code |
| SaveToHTML | Man page Source code |
| SaveToHTML_inner | Source code |
| SelectAndLoadPGM | Source code |
| Study-class | Man page |
| StudyMetaData-class | Man page |
| UserProvidedBiopax | Source code |
| WriteDataWorkUp | Source code |
| WriteSettings | Source code |
| abDrugOverlapAnalysis | Man page Source code |
| addAllPatientOverlaps | Source code |
| addAllPatientSums | Source code |
| addBangForBuck | Man page |
| addBiopaxPath | Source code |
| addCohortToEachIndividual | Source code |
| addCohortToIndividuals | Man page Source code |
| addCorrections | Man page Source code |
| addDbSNPToVariantClassification | Source code |
| addDrugsToGraph | Source code |
| addExperimentalDataToGNEL | Source code |
| addGeneInfo | Source code |
| addImageSlots | Source code |
| addMappingColumn | Source code |
| addMutationCount | Source code |
| addNumberOfPathsTargeted | Source code |
| addPanelMembership | Source code |
| addPathDiagrams | Source code |
| addPathwayImages | Source code |
| addPathwayImagesWithSelection | Man page Source code |
| addPidColumn | Source code |
| addPolyPhenResults | Source code |
| addSequenceCaptureArm | Man page Source code |
| addSignificanceTests | Source code |
| addTable | Source code |
| addToBiopaxRecord | Source code |
| addToPathRecords | Source code |
| addToStyle | Source code |
| adjustColumns | Source code |
| adjustOverlapToSensitive | Source code |
| adjustPathsForCoverage | Source code |
| allInteractiveMainFunction | Man page Source code |
| appendAltNames | Source code |
| appendClincalTrials | Source code |
| appendPPScoresOHSU | Source code Source code |
| applyThreshold | Source code |
| armDescriptionList | Man page Source code |
| armResultsToNozzle | Source code |
| attemptFixSmallMoleculeNames | Source code |
| autoColNamesDataFrame | Source code |
| autoMatrixColNames | Source code |
| autoRowNames | Source code |
| autoRunFromSettings | Man page Source code |
| autoVectorCol | Source code |
| badInput | Source code |
| biopaxFileFromPathName | Source code |
| biopaxFileNameFromPathName | Source code |
| biopaxToGraphNEL | Source code |
| bipartateImport | Source code |
| bmerge | Source code |
| buildGraphNEL | Source code |
| canonicalEdgeNames | Source code |
| changeStudyName | Source code |
| changeStudyNamePrompt | Source code |
| checkAddToCorrectionsFile | Source code |
| checkAndMoveImage | Source code |
| checkColumnNames | Source code |
| checkColums | Source code |
| checkCoverage | Source code |
| checkFileCopyDefault | Man page Source code |
| checkForDups | Source code |
| checkForceRowNames | Source code |
| checkIfDataFame | Source code |
| checkIfMatrix | Source code |
| checkMultipleRecordsOneRepository | Source code |
| checkPathsMatch | Source code |
| checkPreviousCorrections | Source code |
| checkPreviousSymbols | Source code |
| checkRowNames | Source code |
| checkSetDirectoryStructure | Source code |
| checkSummaryTableInput | Source code |
| checkSynonyms | Source code |
| checkUseAlternates | Source code |
| chooseOverlapSet | Source code |
| choosePaths | Source code |
| clean.biopaxRecords | Source code |
| cleanDataFrame | Source code |
| cleanGeneSymbols | Source code |
| cleanMatrix | Source code |
| cleanSyms | Source code |
| cleanTables | Source code |
| cleanVector | Source code |
| clearAllSettings | Source code |
| combineAbSens | Source code |
| combineAberrationTypes | Source code |
| combineAberrationTypes2 | Source code |
| compareSources | Man page Source code |
| corListCheck | Source code |
| coreOverlapAnalysis | Man page Source code |
| coreOverlapAnalysis2 | Source code |
| correctByHgncHelper | Man page Source code |
| correctFromHelperPrevious | Source code |
| corsym | Man page Source code |
| corsym_full | Source code |
| coverageFilePrompt | Source code Source code |
| createGraph | Source code |
| customSlot | Source code |
| customSort | Source code |
| cytoscapePlot | Source code |
| dataCleaningAndCheck | Source code |
| dataType | Source code |
| depricated_getBiomartDbIds | Source code |
| dfToList | Source code |
| downloadHugoLookupTable | Man page |
| edgeList | Source code |
| emptySignature | Source code |
| examineHugoSet | Source code |
| expandToFill | Source code |
| extractAndCleanGeneSymbols | Source code |
| extractCoverageSymbols | Source code |
| extractPathNames | Man page |
| extract_pid | Source code |
| extract_pid_w_matchnormal | Source code |
| extractedDrugScreenAnalysis | Source code |
| filePrompt | Source code Source code |
| filtToPolyPhenTypes | Source code |
| filterByColumn | Source code |
| filterHyperMutators | Source code |
| filterMafToMutsig | Source code |
| filterMutationType | Source code |
| findAllInteractionRows | Source code |
| findInDf | Source code |
| findRows | Source code |
| fixPathNames | Source code |
| formatIDs | Source code |
| formatSettingsToNozzleTable | Source code |
| fromReactome | Source code |
| generalSummary | Source code |
| genesNotInPath | Source code |
| getAllAltNames | Source code |
| getAllDrugGeneAssociations | Source code |
| getAlternateNames | Man page Source code |
| getAndStripHGNC | Source code |
| getBasicSettings | Man page Source code |
| getClinicalRef_depricated | Source code |
| getColorSequence | Source code Source code |
| getComments | Man page Source code |
| getDefaultPaths | Man page Source code |
| getDefaultSettings | Man page Source code |
| getDisplayNames | Source code |
| getDrugData | Source code |
| getDrugEav | Source code |
| getDrugTargetData | Source code |
| getDrugTargetRecords | Source code |
| getEmpP | Source code |
| getFrequencyMatrix | Source code |
| getGenesFromPaths | Man page Source code |
| getHugoSymbols | Man page Source code |
| getHumanPathIds | Man page Source code |
| getKeyedPredictionList | Source code |
| getLoadedPathSummaryRunner | Man page Source code |
| getMinMaxAndFreq | Source code |
| getMutCountMatrix | Source code |
| getNodeNames | Source code |
| getNodePositionTable | Man page Source code |
| getNodePostionTable | Source code |
| getNodes | Source code |
| getNumericScoreColumn | Source code |
| getOfficialGeneIds | Source code |
| getPGM | Source code |
| getPanelCoverage | Source code |
| getPathIdsToTarget | Man page |
| getPathMetaData | Source code |
| getPathObject | Source code |
| getPaths | Man page Source code |
| getPathsForGenes | Source code |
| getPathsWithGenes | Man page Source code |
| getPathwaysRecords | Man page Source code |
| getPatientSubset | Source code Source code |
| getProteinReferenceTable | Source code |
| getPublicationRefs | Man page Source code |
| getReactomeBiopax | Man page Source code |
| getReactomeIds | Man page Source code |
| getRecordsWithNode | Source code |
| getSpaceDividers | Source code |
| getStudies | Source code |
| getStudyObject | Man page Source code |
| getSummaryObject | Source code |
| getSymbolCorrectionTable | Source code |
| getTargetGenesFromDrugs | Source code |
| getTargetMatrix | Source code |
| getTestPGM | Man page Source code |
| getTestPathSummaryRunner | Man page Source code |
| getTestPaths | Source code |
| getTestStudyObject | Man page Source code |
| getTestStudySettings | Man page Source code |
| getUniverse | Source code |
| graphNELToCytoscape | Source code Source code |
| hasAutoColumnNames | Source code |
| htmlPerPatient | Source code |
| htmlSummary | Source code |
| hypergeometricPathEnrichment | Man page |
| importAllGraphite | Man page Source code |
| importDrugDbData | Source code |
| importFromGraphite | Source code |
| importPathways | Source code |
| individualPatientSummary | Source code |
| inferPositions | Source code |
| initiateStudy | Man page Source code |
| installBioconductorPackages | Source code |
| is.error | Source code |
| is.error.message | Source code |
| is.singlevalue | Source code |
| is.uninitilizedNull | Source code |
| isEmpty | Source code |
| isStackedFormat | Source code |
| isSummarySet | Source code |
| joinTables | Source code |
| listToDf | Source code |
| listTypes | Source code |
| list_to_table | Man page Source code |
| loadAllSettings | Source code |
| loadBasicArms | Man page Source code |
| loadClinicalTrailsData | Source code |
| loadCoverageData | Source code Source code |
| loadDataArm | Man page Source code |
| loadDrugEAVtable | Source code |
| loadPathSigTests | Man page Source code |
| loadPaths | Source code |
| loadPathsAsSets | Source code |
| loadPolyPhenResults | Source code |
| loadSettings | Source code |
| loadStudy | Man page Source code |
| loadSummary | Source code |
| logError | Source code |
| longTextBarPlot | Source code |
| makeDrugSelectionWorksheet | Man page Source code |
| makePatientGeneMatrix | Source code |
| makePolyPhenCols | Source code |
| makeSelectNozzleReport | Source code |
| makeStacked | Source code |
| manualPathMetaData | Source code |
| markMultiple | Source code |
| matchTabRow | Source code |
| matrix_to_list | Source code |
| mergeEdges | Source code |
| moveNodeSet | Source code |
| my.file.rename | Source code |
| nestedListToStudy | Source code |
| nodeNamesFromLabels | Man page Source code |
| normalizeDrugTargetsList | Source code |
| notNullOrEmpty | Source code |
| nozzlesToFileStructure | Source code |
| nullOrEmpty | Source code |
| nullOrNoRows | Source code |
| numericThreshold | Source code |
| openPGM | Man page Source code |
| organelleLayout | Source code |
| overlapAnalysisToNozzle | Source code |
| overlapSectionDescriptionDictionary | Source code |
| overlapSectionTitles | Source code |
| overlapSettings | Source code |
| overlapVenn | Source code |
| overlapmerge | Source code |
| paintOverlap | Source code |
| paintPath | Source code |
| parseConsequence | Source code Source code |
| parseConsequenceLong | Source code |
| parseReactomeUniprot | Source code |
| pathSlots | Source code |
| paths | Source code |
| pathsAreFromGraphite | Source code |
| pathwayGraph | Source code |
| pathwaysFromBiopax | Source code |
| patientOverlapToNozzleReport | Source code |
| patientSummaryToNozzleReport | Man page Source code |
| patientSums | Source code |
| patients | Source code |
| pgvmFromStacked | Source code |
| pickSettings | Source code |
| placeDrugs | Source code |
| placeNodesInOrgans | Source code |
| placeOrgans | Source code |
| plotFileName | Source code |
| plotOverlapArea | Source code |
| preProcessPdat | Source code |
| prepDrugSelect | Source code |
| prepPathListForSave | Man page Source code |
| prepareEdges | Source code |
| printNotAvailable | Source code |
| printProgramState | Man page Source code |
| processSequenceCaptureData | Source code |
| processSomaticData | Source code |
| processSomaticDataWithCoverage | Source code |
| pullOutNodeTable | Source code |
| qinfo | Source code |
| reactomeBiomart | Source code |
| readClinicalTrialsFile | Source code |
| readClinicalTrialsFile2 | Source code |
| recordPathSet | Source code |
| removeTabs | Source code |
| remove_dbSNP | Source code |
| resToReport | Source code |
| rowsContaining | Source code |
| runArm | Man page Source code |
| runDrugWorksheet | Man page Source code |
| runMatchedCohort | Source code |
| runMatchedIndividuals | Source code |
| runPanelAnalysis | Source code |
| runSomaticMutationsProcessing | Man page Source code |
| runUnmatchedCohort | Source code |
| runUnmatchedIndividuals | Source code |
| save.plot | Source code |
| saveDataWorkUpNotes | Man page Source code |
| saveDefaultSettings | Source code |
| savePathImageInCytoscape | Source code |
| saveSettings | Source code |
| saveStudy | Man page Source code |
| saveSummary | Source code |
| savestudyMetaData | Source code |
| scaleAndMove | Source code |
| scatterhist | Source code |
| scatterhist2 | Source code |
| sectionDescriptionDictionary | Source code |
| sectionTitles | Source code |
| selectAndLoadResults | Source code |
| selectAndLoadSettings | Man page Source code |
| selectBranchToFindDrugsFor | Source code |
| selectEdges | Source code |
| selectOverlapType | Source code |
| selectStudy | Source code |
| selectionList | Source code |
| sendNetToCytoscape | Source code |
| setAberrationDataStyles | Source code |
| setBiologicalDataStyles | Source code |
| setBorderColors | Man page Source code |
| setColumnPrefix | Source code |
| setCutoff | Man page Source code |
| setDefaultCytoscapeStyle | Source code |
| setDrugScreenCutoff | Source code |
| setEdges | Source code |
| setFunctionalDataStyle | Source code |
| setLayout | Source code |
| setNodeColors | Man page Source code Source code |
| setNodeColors_graphite | Source code |
| setNodeSize | Source code |
| setPathMetaData | Source code |
| setting | Source code |
| settingFile | Source code |
| settingList | Man page Source code |
| settingText | Source code |
| settingsAsDataFrame | Source code |
| settingsDFtreeTolistTree | Source code |
| simpleGGHist | Source code |
| splitMultiGeneRows | Source code |
| splitScoresOut | Source code Source code |
| stackedGeneBar | Source code |
| stackedGeneBar1 | Source code |
| stackedGeneBar_OHSUseq | Source code |
| startHTMLPlugIns | Source code |
| studyFolder | Source code |
| studyName | Source code |
| stylizeDrugs | Source code |
| summarize_by | Man page Source code |
| summaryObjectFromList | Source code |
| summaryTable | Man page Source code |
| summaryTableInner | Source code |
| swapsymbols2 | Source code |
| switchIds | Source code |
| switchPathSymbols | Source code |
| symmetricEdges | Source code |
| targets | Source code |
| test.abDrugOverlapAnalysis | Source code |
| test.fixPathNames | Source code |
| test.getPathIdsToTarget | Source code |
| test.getPaths | Source code |
| test.getReactomeDbIds | Source code |
| test.makeDrugSelectionWorksheet | Source code |
| test.prepPathListForSave | Source code |
| test.recordPathSet | Source code |
| test.saveDataWorkUpNotes | Source code |
| test.savePathImageInCytoscape | Source code |
| test.selectBranchToFindDrugsFor | Source code |
| test.selectStudy | Source code |
| test.sendNetToCytoscape | Source code |
| test.setAberrationDataStyles | Source code |
| test.settingFile | Source code |
| test.settingList | Source code |
| test.summarize_by | Source code |
| test.toGSEAformat | Source code |
| test.twoHistOnePlot | Source code |
| testGetPathListObject | Source code |
| textThreshold | Source code |
| toBipartateGraph | Source code |
| toGSEAclinical | Source code |
| toGSEAformat | Source code |
| toHTML | Source code |
| toPGM | Source code |
| toPGMWithCoverage | Source code |
| top20Hists | Source code |
| trimTable | Source code |
| twoHistOnePlot | Man page Source code |
| unfactorize | Man page |
| whichPaths | Man page Source code |
