Files in nuno-agostinho/psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
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_local.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_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_psichomicsGeneExpression.R R/formats_psichomicsInclusionLevels.R R/globalAccess.R R/groups.R R/help.R R/utils.R README.md
appveyor.yml
codecov.yml
inst/extdata/TCGAsampleType.RDS
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT3.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT5.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.COMBI.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.EXSK.Template.2.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.IR.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MERGE3m.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MIC.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MULTI.Template.2.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A3SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A5SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.AFE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.ALE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.MXE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.SE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A3SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A5SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.AFE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.ALE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.MXE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.SE.txt
inst/extdata/eventsAnnotSample/miso_annotation/A3SS.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/A5SS.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/AFE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/ALE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/MXE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/RI.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/SE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/TandemUTR.hg19.gff3
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A3.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A5.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AF.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AL.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_MX.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_RI.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_SE.ioe
inst/extdata/ex_gene_expression.RDS
inst/extdata/ex_junctionQuant.RDS
inst/extdata/ex_splicing_annotation.RDS
inst/extdata/miso_AS_annot_example.gff3
inst/shiny/www/animate.min.css
inst/shiny/www/functions.js
inst/shiny/www/fuzzy.min.js
inst/shiny/www/highcharts.ext.js
inst/shiny/www/jquery.textcomplete.min.js
inst/shiny/www/set-operations/css/set-operations.css
inst/shiny/www/set-operations/fonts/set-operations.eot
inst/shiny/www/set-operations/fonts/set-operations.svg
inst/shiny/www/set-operations/fonts/set-operations.ttf
inst/shiny/www/set-operations/fonts/set-operations.woff
inst/shiny/www/styles.css
inst/shiny/www/validator.min.js
man/ASquantFileInput.Rd man/addTCGAdata.Rd man/appServer.Rd man/appUI.Rd man/appendNewGroups.Rd man/articleUI.Rd man/assignColours.Rd man/basicStats.Rd man/blendColours.Rd man/browserHistory.Rd man/bsModal2.Rd man/calculateInclusionLevels.Rd man/checkFileFormat.Rd man/checkFirebrowse.Rd man/checkIntegrity.Rd man/checkSurvivalInput.Rd man/closeProgress.Rd man/clusterICAset.Rd man/clusterSet.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/diffAnalyses.Rd man/diffAnalysesPlotSet.Rd man/diffAnalysesSet.Rd man/diffAnalysesTableSet.Rd man/diffExpressionPlotSet.Rd man/diffExpressionSet.Rd man/diffExpressionTableSet.Rd man/disableTab.Rd man/display.Rd man/downloadFiles.Rd man/endProcess.Rd man/ensemblToUniprot.Rd man/escape.Rd man/eventPlotOptions.Rd man/export_highcharts.Rd man/fileBrowser.Rd man/fileBrowserInput.Rd man/filterGroups.Rd man/fisher.Rd man/fligner.Rd man/geNormalisationFilteringInterface.Rd man/geneExprFileInput.Rd man/geneExprSurvSet.Rd man/getASevent.Rd man/getASevents.Rd man/getAttributesTime.Rd man/getClinicalDataForSurvival.Rd man/getClinicalMatchFrom.Rd man/getData.Rd man/getDataRows.Rd man/getDifferentialAnalyses.Rd man/getDifferentialExpression.Rd man/getDownloadsFolder.Rd man/getEvent.Rd man/getFirebrowseCohorts.Rd man/getFirebrowseDataTypes.Rd man/getFirebrowseDateFormat.Rd man/getFirebrowseDates.Rd man/getGenes.Rd man/getGenesFromSplicingEvents.Rd man/getGlobal.Rd man/getGroups.Rd man/getGtexTissues.Rd man/getHidden.Rd man/getHighlightedPoints.Rd man/getMatchingSamples.Rd man/getNumerics.Rd man/getPatientFromSample.Rd man/getServerFunctions.Rd man/getSplicingEventCoordinates.Rd man/getSplicingEventFromGenes.Rd man/getSplicingEventTypes.Rd man/getUiFunctions.Rd man/getValidEvents.Rd man/getValuePerPatient.Rd man/ggplotServer.Rd man/ggplotTooltip.Rd man/ggplotUI.Rd man/globalSelectize.Rd man/groupByAttribute.Rd man/groupByExpression.Rd man/groupByGrep.Rd man/groupById.Rd man/groupManipulation.Rd man/groupManipulationInput.Rd man/groupPerElem.Rd man/groupsServerOnce.Rd man/hc_scatter.Rd man/hchart.survfit.Rd man/inclusionLevelsInterface.Rd man/inlineDialog.Rd man/insideFile.Rd man/is.whole.Rd man/isFirebrowseUp.Rd man/joinEventsPerType.Rd man/junctionString.Rd man/kruskal.Rd man/labelBasedOnCutoff.Rd man/levene.Rd man/leveneTest.Rd man/listAllAnnotations.Rd man/listSplicingAnnotations.Rd man/loadAnnotation.Rd man/loadBy.Rd man/loadCustomSplicingAnnotationSet.Rd man/loadFile.Rd man/loadFileFormats.Rd man/loadFirebrowseData.Rd man/loadFirebrowseFolders.Rd man/loadGeneExpressionSet.Rd man/loadGtexData.Rd man/loadGtexDataShiny.Rd man/loadGtexFile.Rd man/loadLocalFiles.Rd man/loadSplicingQuantificationSet.Rd man/loadTCGAsampleMetadata.Rd man/loadedDataModal.Rd man/matchPatientToSingleSample.Rd man/matchSplicingEventsWithGenes.Rd man/missingDataModal.Rd man/modTabPanel.Rd man/navSelectize.Rd man/noinfo.Rd man/normaliseGeneExpression.Rd man/operateOnGroups.Rd man/optimSurvDiffSet.Rd man/optimalPSIcutoff.Rd man/parseCategoricalGroups.Rd man/parseDateResponse.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/parseSampleGroups.Rd man/parseSplicingEvent.Rd man/parseSuppaEvent.Rd man/parseSuppaGeneric.Rd man/parseTcgaSampleInfo.Rd man/parseUniprotXML.Rd man/parseUrlsFromFirebrowseResponse.Rd man/parseValidFile.Rd man/parseVastToolsEvent.Rd man/parseVastToolsSE.Rd man/performICA.Rd man/performPCA.Rd man/plotClusters.Rd man/plotCorrelation.Rd man/plotDistribution.Rd man/plotGroupIndependence.Rd man/plotICA.Rd man/plotPCA.Rd man/plotPointsStyle.Rd man/plotProtein.Rd man/plotSingleICA.Rd man/plotSurvivalCurves.Rd man/plotTranscripts.Rd man/plotVariance.Rd man/plottableXranges.Rd man/prepareAnnotationFromEvents.Rd man/prepareEventPlotOptions.Rd man/prepareFileBrowser.Rd man/prepareFirebrowseArchives.Rd man/processButton.Rd man/processDatasetNames.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/queryEnsemblByEvent.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/renderDataTableSparklines.Rd man/renderGeneticInfo.Rd man/renderGroupInterface.Rd man/renderProteinInfo.Rd man/rm.null.Rd man/roundDigits.Rd man/rowMeans.Rd man/rowVars.Rd man/selectGroupsUI.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/spearman.Rd man/startProcess.Rd man/startProgress.Rd man/styleModal.Rd man/survdiff.survTerms.Rd man/survfit.survTerms.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/transformData.Rd man/transformOptions.Rd man/transformValues.Rd man/trimWhitespace.Rd man/ttest.Rd man/uniqueBy.Rd man/updateClinicalParams.Rd man/updateFileBrowserInput.Rd man/updateProgress.Rd man/vennEvents.Rd man/wilcox.Rd
psichomics.Rproj
screenshot.png
tests/testthat.R tests/testthat/testCorrelationGEandAS.R tests/testthat/testDifferentialSplicing.R tests/testthat/testFilterGroups.R tests/testthat/testFirebrowse.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/testRenameDuplicated.R tests/testthat/testRowVar.R tests/testthat/testSuppaEvents.R tests/testthat/testSurvival.R tests/testthat/testUtils.R tests/testthat/testVastToolsEvents.R vignettes/AS_events_preparation.Rmd
vignettes/BRCA_clinical.RDS
vignettes/BRCA_geneExpr.RDS
vignettes/BRCA_psi.RDS
vignettes/CLI_tutorial.Rmd vignettes/GUI_tutorial.Rmd
vignettes/img/1_load_data.png
vignettes/img/2_quantify_splicing.png
vignettes/img/3_survival.png
vignettes/img/4_pca.png
vignettes/img/5_psi_cutoff_2.png
vignettes/img/6_diff_splicing.png
vignettes/img/7_psi_cutoff.png
vignettes/refs.bib
nuno-agostinho/psichomics documentation built on Nov. 1, 2017, 3:18 p.m.