Files in nuno-agostinho/psichomics

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

CONDUCT.md NEWS.md R/RcppExports.R R/analysis.R R/analysis_correlation.R R/analysis_diffExpression.R R/analysis_diffExpression_event.R R/analysis_diffExpression_table.R R/analysis_diffSplicing.R R/analysis_diffSplicing_event.R R/analysis_diffSplicing_table.R R/analysis_dimReduction.R R/analysis_dimReduction_ica.R R/analysis_dimReduction_pca.R R/analysis_information.R R/analysis_survival.R R/analysis_template.R R/app.R R/data.R R/data_firebrowse.R R/data_geNormalisationFiltering.R R/data_gtex.R R/data_inclusionLevels.R R/data_inclusionLevelsFilter.R R/data_local.R R/data_recount.R R/events.R R/events_mats.R R/events_miso.R R/events_suppa.R R/events_vastTools.R R/formats.R R/formats_SraRunTableSampleInfo.R R/formats_firebrowseGeneExpression.R R/formats_firebrowseJunctionReads.R R/formats_firebrowseMergeClinical.R R/formats_firebrowseNormalizedGeneExpression.R R/formats_genericClinical.R R/formats_genericGeneExpression.R R/formats_genericInclusionLevels.R R/formats_genericJunctionReads.R R/formats_genericSampleInfo.R R/formats_gtexClinical.R R/formats_gtexGeneReadsFormat.R R/formats_gtexJunctionReads.R R/formats_gtexSampleInfo.R R/formats_gtexV7Clinical.R R/formats_gtexV7JunctionReads.R R/formats_gtexV8JunctionReads.R R/formats_psichomicsGeneExpression.R R/formats_psichomicsInclusionLevels.R R/formats_recountSampleInfo.R R/formats_vasttoolsGeneExpression.R R/formats_vasttoolsInclusionLevels.R R/formats_vasttoolsInclusionLevelsTidy.R R/globalAccess.R R/groups.R R/help.R R/utils.R R/utils_drawSplicingEvent.R R/utils_eventParsing.R R/utils_fileBrowserDialog.R R/utils_interactiveGgplot.R R/utils_interface.R README.md dev/event_diagrams.R dev/survival_analysis.R man/HTMLfast.Rd man/addObjectAttrs.Rd man/addTCGAdata.Rd man/analysesTableSet.Rd man/appServer.Rd man/appUI.Rd man/appendNewGroups.Rd man/areSplicingEvents.Rd man/articleUI.Rd man/assignColours.Rd man/assignValuePerSubject.Rd man/basicStats.Rd man/blendColours.Rd man/browseDownloadFolderInput.Rd man/browserHistory.Rd man/calculateInclusionLevels.Rd man/calculateLoadingsContribution.Rd man/checkFileFormat.Rd man/checkFirebrowse.Rd man/checkGroupType.Rd man/checkIntegrity.Rd man/checkSurvivalInput.Rd man/clusterICAset.Rd man/clusterSet.Rd man/colSums-EList-method.Rd man/colourInputMod.Rd man/convertGeneIdentifiers.Rd man/correlateGEandAS.Rd man/createDataTab.Rd man/createDensitySparklines.Rd man/createEventPlotting.Rd man/createGroup.Rd man/createGroupByAttribute.Rd man/createGroupById.Rd man/createGroupFromInput.Rd man/createJunctionsTemplate.Rd man/createOptimalSurvData.Rd man/createSparklines.Rd man/customRowMeans.Rd man/diagramSplicingEvent.Rd man/diffAnalyses.Rd man/diffExpressionSet.Rd man/diffSplicingSet.Rd man/disableTab.Rd man/discardLowCoveragePSIvalues.Rd man/discardOutsideSamplesFromGroups.Rd man/display.Rd man/dot-onAttach.Rd man/downloadFiles.Rd man/ensemblToUniprot.Rd man/escape.Rd man/eventPlotOptions.Rd man/exportGroupsToFile.Rd man/export_highcharts.Rd man/fileBrowser.Rd man/fileBrowserInput.Rd man/filterGeneExpr.Rd man/filterGroups.Rd man/filterPSI.Rd man/findASeventsFromGene.Rd man/findEventData.Rd man/geNormalisationFilteringInterface.Rd man/geneExprFileInput.Rd man/geneExprSurvSet.Rd man/getAttributesTime.Rd man/getClinicalDataForSurvival.Rd man/getClinicalMatchFrom.Rd man/getData.Rd man/getDataRows.Rd man/getDifferentialExpression.Rd man/getDifferentialSplicing.Rd man/getDownloadsFolder.Rd man/getFirebrowseDateFormat.Rd man/getGeneList.Rd man/getGlobal.Rd man/getGroups.Rd man/getGtexDataTypes.Rd man/getGtexDataURL.Rd man/getGtexTissues.Rd man/getHidden.Rd man/getHighlightedPoints.Rd man/getNumerics.Rd man/getSampleFromSubject.Rd man/getSelectedDataPanel.Rd man/getServerFunctions.Rd man/getSplicingEventCoordinates.Rd man/getSplicingEventData.Rd man/getSplicingEventFromGenes.Rd man/getSplicingEventTypes.Rd man/getSubjectFromSample.Rd man/getTCGAdataTypes.Rd man/getUiFunctions.Rd man/getValidEvents.Rd man/ggplotServer.Rd man/ggplotTooltip.Rd man/ggplotUI.Rd man/globalSelectize.Rd man/groupByAttribute.Rd man/groupManipulation.Rd man/groupManipulationInput.Rd man/groupPerElem.Rd man/groupsServerOnce.Rd man/hc_scatter.Rd man/hchart.survfit.Rd man/importGroupsFrom.Rd man/inclusionLevelsFilterInterface.Rd man/inclusionLevelsInterface.Rd man/inlineDialog.Rd man/insideFile.Rd man/is.whole.Rd man/isFile.Rd man/isFirebrowseUp.Rd man/isRStudioServer.Rd man/joinEventsPerType.Rd man/junctionString.Rd man/labelBasedOnCutoff.Rd man/leveneTest.Rd man/linkToArticles.Rd man/linkToRunJS.Rd man/listAllAnnotations.Rd man/listSplicingAnnotations.Rd man/loadAnnotation.Rd man/loadAnnotationHub.Rd man/loadBy.Rd man/loadCustomSplicingAnnotationSet.Rd man/loadFile.Rd man/loadFileFormats.Rd man/loadFirebrowseFolders.Rd man/loadGeneExpressionSet.Rd man/loadGtexData.Rd man/loadGtexDataShiny.Rd man/loadGtexFile.Rd man/loadLocalFiles.Rd man/loadSRAproject.Rd man/loadSplicingQuantificationSet.Rd man/loadTCGAdata.Rd man/loadTCGAsampleMetadata.Rd man/loadedDataModal.Rd man/matchGroupASeventsAndGenes.Rd man/matchGroupSubjectsAndSamples.Rd man/matchSplicingEventsWithGenes.Rd man/missingDataModal.Rd man/modTabPanel.Rd man/navSelectize.Rd man/normaliseGeneExpression.Rd man/operateOnGroups.Rd man/optimSurvDiffSet.Rd man/optimalSurvivalCutoff.Rd man/parseCategoricalGroups.Rd man/parseDateResponse.Rd man/parseFile.Rd man/parseFirebrowseMetadata.Rd man/parseMatsEvent.Rd man/parseMatsGeneric.Rd man/parseMisoAnnotation.Rd man/parseMisoEvent.Rd man/parseMisoEventID.Rd man/parseMisoGeneric.Rd man/parseMisoId.Rd man/parseSplicingEvent.Rd man/parseSuppaEvent.Rd man/parseSuppaGeneric.Rd man/parseTcgaSampleInfo.Rd man/parseUniprotXML.Rd man/parseUrlsFromFirebrowseResponse.Rd man/parseVastToolsEvent.Rd man/parseVastToolsSE.Rd man/performICA.Rd man/performPCA.Rd man/plot.GEandAScorrelation.Rd man/plotClusters.Rd man/plotDistribution.Rd man/plotGeneExprPerSample.Rd man/plotGroupIndependence.Rd man/plotICA.Rd man/plotLibrarySize.Rd man/plotPCA.Rd man/plotPCAvariance.Rd man/plotPointsStyle.Rd man/plotProtein.Rd man/plotRowStats.Rd man/plotSingleICA.Rd man/plotSplicingEvent.Rd man/plotSurvivalCurves.Rd man/plotSurvivalPvaluesByCutoff.Rd man/plotTranscripts.Rd man/plottableXranges.Rd man/prepareAnnotationFromEvents.Rd man/prepareEventPlotOptions.Rd man/prepareFileBrowser.Rd man/prepareFirebrowseArchives.Rd man/prepareGenePresentation.Rd man/prepareJunctionQuantSTAR.Rd man/preparePreMadeGroupForSelection.Rd man/prepareSRAmetadata.Rd man/prepareWordBreak.Rd man/preserveAttributes.Rd man/processButton.Rd man/processDatasetNames.Rd man/processSRAdata.Rd man/processSurvData.Rd man/processSurvTerms.Rd man/processSurvival.Rd man/psichomics.Rd man/pubmedUI.Rd man/quantifySplicing.Rd man/quantifySplicingSet.Rd man/queryEnsembl.Rd man/queryEnsemblByGene.Rd man/queryFirebrowseData.Rd man/queryPubMed.Rd man/queryUniprot.Rd man/readAnnot.Rd man/readFile.Rd man/reduceDimensionality.Rd man/renameDuplicated.Rd man/renameGroups.Rd man/renderBoxplot.Rd man/renderDataTableSparklines.Rd man/renderGeneticInfo.Rd man/renderGroupInterface.Rd man/renderProteinInfo.Rd man/replaceStrInList.Rd man/rm.null.Rd man/roundDigits.Rd man/roundMinDown.Rd man/saveProcessedSRAdata.Rd man/selectGroupsUI.Rd man/selectPreMadeGroup.Rd man/selectizeGeneInput.Rd man/setFirebrowseData.Rd man/setLocalData.Rd man/setOperation.Rd man/setOperationIcon.Rd man/showAlert.Rd man/showGroupsTable.Rd man/sidebar.Rd man/signifDigits.Rd man/singleDiffAnalyses.Rd man/sortCoordinates.Rd man/startProcess.Rd man/startProgress.Rd man/styleModal.Rd man/subjectMultiMatchWarning.Rd man/subsetGeneExpressionFromMatchingGenes.Rd man/survdiffTerms.Rd man/survfit.survTerms.Rd man/t.sticky.Rd man/tabDataset.Rd man/table2html.Rd man/tableRow.Rd man/testGroupIndependence.Rd man/testSingleIndependence.Rd man/testSurvival.Rd man/testSurvivalCutoff.Rd man/textSuggestions.Rd man/toJSarray.Rd man/traceInList.Rd man/transformData.Rd man/transformOptions.Rd man/transformValues.Rd man/trimWhitespace.Rd man/uniqueBy.Rd man/updateClinicalParams.Rd man/updateFileBrowserInput.Rd man/vennEvents.Rd man/wilcox.Rd tests/spelling.R tests/testthat.R tests/testthat/testCorrelationGEandAS.R tests/testthat/testCustomDataLoading.R tests/testthat/testDifferentialSplicing.R tests/testthat/testDiscardLowCoveragePSIs.R tests/testthat/testFileFormats.R tests/testthat/testFilterGroups.R tests/testthat/testFirebrowse.R tests/testthat/testGTEx.R tests/testthat/testGeneInfo.R tests/testthat/testGroups.R tests/testthat/testICA.R tests/testthat/testLeveneTest.R tests/testthat/testLoadBy.R tests/testthat/testMatsEvents.R tests/testthat/testMisoEvents.R tests/testthat/testPCA.R tests/testthat/testPSIquantification.R tests/testthat/testPlotSplicingEvent.R tests/testthat/testRenameDuplicated.R tests/testthat/testRowVar.R tests/testthat/testSRAloading.R tests/testthat/testSticky.R tests/testthat/testSuppaEvents.R tests/testthat/testSurvival.R tests/testthat/testUtils.R tests/testthat/testVastToolsEvents.R vignettes/AS_events_preparation.Rmd vignettes/CLI_tutorial.Rmd vignettes/GUI_tutorial.Rmd vignettes/custom_data.Rmd