Files in psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
NEWS.md
README.md
psichomics documentation built on Nov. 8, 2020, 5:44 p.m.
NAMESPACE
DESCRIPTION
LICENSE
build/vignette.rds
src/RcppExports.cpp
src/psiFastCalc.cpp
R/events.R
R/utils_eventParsing.R
R/formats_gtexJunctionReads.R
R/globalAccess.R
R/analysis_dimReduction_ica.R
R/formats_recountSampleInfo.R
R/formats_gtexSampleInfo.R
R/events_vastTools.R
R/formats_genericInclusionLevels.R
R/analysis_dimReduction_pca.R
R/formats_firebrowseMergeClinical.R
R/utils_drawSplicingEvent.R
R/formats.R
R/formats_firebrowseNormalizedGeneExpression.R
R/formats_genericJunctionReads.R
R/utils_fileBrowserDialog.R
R/data_inclusionLevels.R
R/data_firebrowse.R
R/help.R
R/analysis_diffSplicing_event.R
R/RcppExports.R
R/utils.R
R/formats_gtexV8JunctionReads.R
R/analysis_diffSplicing.R
R/analysis_information.R
R/formats_vasttoolsInclusionLevels.R
R/formats_gtexV7Clinical.R
R/formats_genericClinical.R
R/formats_firebrowseJunctionReads.R
R/formats_psichomicsInclusionLevels.R
R/analysis_diffExpression_event.R
R/data_gtex.R
R/analysis_template.R
R/formats_genericSampleInfo.R
R/formats_vasttoolsGeneExpression.R
R/utils_interactiveGgplot.R
R/app.R
R/formats_psichomicsGeneExpression.R
R/analysis_diffSplicing_table.R
R/analysis_diffExpression_table.R
R/analysis_correlation.R
R/events_mats.R
R/formats_gtexV7JunctionReads.R
R/analysis_dimReduction.R
R/data_recount.R
R/data_geNormalisationFiltering.R
R/events_miso.R
R/formats_gtexGeneReadsFormat.R
R/formats_gtexClinical.R
R/analysis.R
R/data_inclusionLevelsFilter.R
R/analysis_diffExpression.R
R/formats_SraRunTableSampleInfo.R
R/data.R
R/groups.R
R/formats_firebrowseGeneExpression.R
R/formats_vasttoolsInclusionLevelsTidy.R
R/data_local.R
R/events_suppa.R
R/utils_interface.R
R/formats_genericGeneExpression.R
R/analysis_survival.R
vignettes/custom_data.Rmd
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/refs.bib
vignettes/bioinformatics.csl
vignettes/img/5_pca.png
vignettes/img/diff_analyses.png
vignettes/img/NUMB_exon_12_inclusion.png
vignettes/img/UHRF2_exon_10_inclusion_prognosis.png
vignettes/img/4_group_tables.png
vignettes/img/UHRF2_expression_prognosis.png
vignettes/img/pca_results.png
vignettes/img/UHRF2_differential_expression.png
vignettes/img/4_save_groups.png
vignettes/img/Correlation_NUMB_exon_12_and_QKI_GE.png
vignettes/img/3_quantify_splicing.png
vignettes/img/2_normalise_gene_expression.png
vignettes/img/4_data_grouping.png
vignettes/img/1_load_data.png
vignettes/img/4_survival.png
vignettes/img/diff_expression.png
vignettes/img/UHRF2_exon_10_inclusion_differential_splicing.png
man/listSplicingAnnotations.Rd
man/groupsServerOnce.Rd
man/plotTranscripts.Rd
man/renameGroups.Rd
man/parseFile.Rd
man/subsetGeneExpressionFromMatchingGenes.Rd
man/transformData.Rd
man/survdiffTerms.Rd
man/findEventData.Rd
man/getUiFunctions.Rd
man/loadBy.Rd
man/loadedDataModal.Rd
man/parseMisoEvent.Rd
man/inlineDialog.Rd
man/getGroups.Rd
man/testSurvival.Rd
man/disableTab.Rd
man/importGroupsFrom.Rd
man/calculateLoadingsContribution.Rd
man/assignValuePerSubject.Rd
man/isFile.Rd
man/getClinicalDataForSurvival.Rd
man/checkGroupType.Rd
man/customRowMeans.Rd
man/getSplicingEventFromGenes.Rd
man/parseVastToolsEvent.Rd
man/HTMLfast.Rd
man/checkIntegrity.Rd
man/assignColours.Rd
man/readFile.Rd
man/signifDigits.Rd
man/parseUniprotXML.Rd
man/eventPlotOptions.Rd
man/plotICA.Rd
man/getDownloadsFolder.Rd
man/groupPerElem.Rd
man/getGeneList.Rd
man/plotSplicingEvent.Rd
man/prepareFirebrowseArchives.Rd
man/discardOutsideSamplesFromGroups.Rd
man/renderDataTableSparklines.Rd
man/parseMisoAnnotation.Rd
man/plotProtein.Rd
man/ggplotUI.Rd
man/joinEventsPerType.Rd
man/getFirebrowseDateFormat.Rd
man/plotPointsStyle.Rd
man/processDatasetNames.Rd
man/plotGeneExprPerSample.Rd
man/groupManipulation.Rd
man/getNumerics.Rd
man/subjectMultiMatchWarning.Rd
man/groupManipulationInput.Rd
man/loadSplicingQuantificationSet.Rd
man/ggplotServer.Rd
man/labelBasedOnCutoff.Rd
man/prepareFileBrowser.Rd
man/globalSelectize.Rd
man/articleUI.Rd
man/parseSplicingEvent.Rd
man/calculateInclusionLevels.Rd
man/getValidEvents.Rd
man/getClinicalMatchFrom.Rd
man/tableRow.Rd
man/parseFirebrowseMetadata.Rd
man/plotRowStats.Rd
man/parseMatsGeneric.Rd
man/plotSurvivalCurves.Rd
man/getTCGAdataTypes.Rd
man/optimSurvDiffSet.Rd
man/appendNewGroups.Rd
man/hc_scatter.Rd
man/getDifferentialSplicing.Rd
man/setFirebrowseData.Rd
man/optimalSurvivalCutoff.Rd
man/createGroupById.Rd
man/plottableXranges.Rd
man/plotSurvivalPvaluesByCutoff.Rd
man/testSingleIndependence.Rd
man/appUI.Rd
man/filterGeneExpr.Rd
man/selectGroupsUI.Rd
man/plotPCA.Rd
man/getGtexTissues.Rd
man/setLocalData.Rd
man/blendColours.Rd
man/createGroup.Rd
man/pubmedUI.Rd
man/renameDuplicated.Rd
man/vennEvents.Rd
man/loadTCGAdata.Rd
man/getGtexDataURL.Rd
man/performPCA.Rd
man/sortCoordinates.Rd
man/clusterSet.Rd
man/quantifySplicing.Rd
man/processButton.Rd
man/display.Rd
man/createEventPlotting.Rd
man/createDensitySparklines.Rd
man/parseMatsEvent.Rd
man/transformOptions.Rd
man/styleModal.Rd
man/checkSurvivalInput.Rd
man/renderGeneticInfo.Rd
man/diffExpressionSet.Rd
man/inclusionLevelsInterface.Rd
man/loadAnnotation.Rd
man/psichomics.Rd
man/selectPreMadeGroup.Rd
man/junctionString.Rd
man/parseTcgaSampleInfo.Rd
man/listAllAnnotations.Rd
man/preserveAttributes.Rd
man/loadGtexData.Rd
man/checkFirebrowse.Rd
man/dot-onAttach.Rd
man/createSparklines.Rd
man/table2html.Rd
man/setOperation.Rd
man/showGroupsTable.Rd
man/isRStudioServer.Rd
man/normaliseGeneExpression.Rd
man/getDifferentialExpression.Rd
man/fileBrowser.Rd
man/exportGroupsToFile.Rd
man/showAlert.Rd
man/parseCategoricalGroups.Rd
man/leveneTest.Rd
man/getHidden.Rd
man/clusterICAset.Rd
man/roundDigits.Rd
man/getSplicingEventTypes.Rd
man/testGroupIndependence.Rd
man/getSplicingEventCoordinates.Rd
man/export_highcharts.Rd
man/createGroupFromInput.Rd
man/checkFileFormat.Rd
man/isFirebrowseUp.Rd
man/parseUrlsFromFirebrowseResponse.Rd
man/parseMisoId.Rd
man/updateClinicalParams.Rd
man/geneExprSurvSet.Rd
man/startProgress.Rd
man/parseSuppaGeneric.Rd
man/colourInputMod.Rd
man/queryUniprot.Rd
man/loadTCGAsampleMetadata.Rd
man/prepareGenePresentation.Rd
man/correlateGEandAS.Rd
man/loadSRAproject.Rd
man/diffAnalyses.Rd
man/getSampleFromSubject.Rd
man/queryPubMed.Rd
man/convertGeneIdentifiers.Rd
man/getGlobal.Rd
man/textSuggestions.Rd
man/browserHistory.Rd
man/testSurvivalCutoff.Rd
man/setOperationIcon.Rd
man/prepareJunctionQuantSTAR.Rd
man/getGtexDataTypes.Rd
man/prepareWordBreak.Rd
man/survfit.survTerms.Rd
man/plotClusters.Rd
man/insideFile.Rd
man/basicStats.Rd
man/renderProteinInfo.Rd
man/createDataTab.Rd
man/addObjectAttrs.Rd
man/downloadFiles.Rd
man/diagramSplicingEvent.Rd
man/getSubjectFromSample.Rd
man/ggplotTooltip.Rd
man/renderBoxplot.Rd
man/operateOnGroups.Rd
man/getServerFunctions.Rd
man/escape.Rd
man/geNormalisationFilteringInterface.Rd
man/loadFile.Rd
man/startProcess.Rd
man/navSelectize.Rd
man/renderGroupInterface.Rd
man/processSurvival.Rd
man/loadGtexFile.Rd
man/getData.Rd
man/getHighlightedPoints.Rd
man/hchart.survfit.Rd
man/parseVastToolsSE.Rd
man/linkToRunJS.Rd
man/missingDataModal.Rd
man/toJSarray.Rd
man/getSplicingEventData.Rd
man/parseSuppaEvent.Rd
man/filterPSI.Rd
man/loadGtexDataShiny.Rd
man/processSRAdata.Rd
man/performICA.Rd
man/prepareEventPlotOptions.Rd
man/queryEnsemblByGene.Rd
man/modTabPanel.Rd
man/matchGroupASeventsAndGenes.Rd
man/reduceDimensionality.Rd
man/roundMinDown.Rd
man/plotLibrarySize.Rd
man/singleDiffAnalyses.Rd
man/saveProcessedSRAdata.Rd
man/createJunctionsTemplate.Rd
man/diffSplicingSet.Rd
man/selectizeGeneInput.Rd
man/getAttributesTime.Rd
man/appServer.Rd
man/findASeventsFromGene.Rd
man/areSplicingEvents.Rd
man/ASquantFileInput.Rd
man/preparePreMadeGroupForSelection.Rd
man/wilcox.Rd
man/inclusionLevelsFilterInterface.Rd
man/matchGroupSubjectsAndSamples.Rd
man/loadLocalFiles.Rd
man/parseDateResponse.Rd
man/is.whole.Rd
man/t.sticky.Rd
man/filterGroups.Rd
man/parseMisoGeneric.Rd
man/queryFirebrowseData.Rd
man/discardLowCoveragePSIvalues.Rd
man/matchSplicingEventsWithGenes.Rd
man/plotGroupIndependence.Rd
man/plotDistribution.Rd
man/readAnnot.Rd
man/queryEnsembl.Rd
man/analysesTableSet.Rd
man/groupByAttribute.Rd
man/addTCGAdata.Rd
man/sidebar.Rd
man/tabDataset.Rd
man/uniqueBy.Rd
man/processSurvData.Rd
man/ensemblToUniprot.Rd
man/createOptimalSurvData.Rd
man/loadGeneExpressionSet.Rd
man/prepareSRAmetadata.Rd
man/loadCustomSplicingAnnotationSet.Rd
man/loadFirebrowseFolders.Rd
man/quantifySplicingSet.Rd
man/trimWhitespace.Rd
man/transformValues.Rd
man/parseMisoEventID.Rd
man/geneExprFileInput.Rd
man/loadFileFormats.Rd
man/prepareAnnotationFromEvents.Rd
man/fileBrowserInput.Rd
man/plotPCAvariance.Rd
man/rm.null.Rd
man/updateFileBrowserInput.Rd
man/plot.GEandAScorrelation.Rd
man/processSurvTerms.Rd
man/colSums-EList-method.Rd
man/getDataRows.Rd
man/plotSingleICA.Rd
man/createGroupByAttribute.Rd
man/linkToArticles.Rd
man/figures/screenshot.png
tests/testthat.R
tests/spelling.R
tests/testthat/testPlotSplicingEvent.R
tests/testthat/testSticky.R
tests/testthat/testGroups.R
tests/testthat/testMisoEvents.R
tests/testthat/testICA.R
tests/testthat/testDifferentialSplicing.R
tests/testthat/testGeneInfo.R
tests/testthat/testPSIquantification.R
tests/testthat/testSurvival.R
tests/testthat/testLeveneTest.R
tests/testthat/testCorrelationGEandAS.R
tests/testthat/testCustomDataLoading.R
tests/testthat/testMatsEvents.R
tests/testthat/testSRAloading.R
tests/testthat/testFirebrowse.R
tests/testthat/testRowVar.R
tests/testthat/testVastToolsEvents.R
tests/testthat/testUtils.R
tests/testthat/testFilterGroups.R
tests/testthat/testFileFormats.R
tests/testthat/testLoadBy.R
tests/testthat/testPCA.R
tests/testthat/testSuppaEvents.R
tests/testthat/testRenameDuplicated.R
tests/testthat/data/vasttools_incLevels.tab
tests/testthat/data/vasttools_cRPKM.tab
tests/testthat/data/vasttools_cRPKM_AND_COUNTS.tab
tests/testthat/data/sraMetadata.txt
inst/CITATION
inst/WORDLIST
inst/doc/GUI_tutorial.html
inst/doc/AS_events_preparation.R
inst/doc/AS_events_preparation.html
inst/doc/custom_data.Rmd
inst/doc/GUI_tutorial.R
inst/doc/AS_events_preparation.Rmd
inst/doc/CLI_tutorial.html
inst/doc/custom_data.R
inst/doc/CLI_tutorial.R
inst/doc/CLI_tutorial.Rmd
inst/doc/custom_data.html
inst/doc/GUI_tutorial.Rmd
inst/shiny/www/jquery.mark.min.js
inst/shiny/www/psichomics.css
inst/shiny/www/animate.min.css
inst/shiny/www/psichomics.js
inst/shiny/www/highcharts.ext.js
inst/shiny/www/fuzzy.min.js
inst/shiny/www/jquery.textcomplete.min.js
inst/shiny/www/set-operations/fonts/set-operations.woff
inst/shiny/www/set-operations/fonts/set-operations.ttf
inst/shiny/www/set-operations/fonts/set-operations.eot
inst/shiny/www/set-operations/fonts/set-operations.svg
inst/shiny/www/set-operations/css/set-operations.css
inst/extdata/ex_junctionQuant.RDS
inst/extdata/TCGAsampleType.RDS
inst/extdata/ex_gene_expression.RDS
inst/extdata/ex_splicing_annotation.RDS
inst/extdata/miso_AS_annot_example.gff3
inst/extdata/Sebestyen_et_al_2016.RDS
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.SE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.SE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A5SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.MXE.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.A3SS.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.A3SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.MXE.txt
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_MX.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_SE.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_A3.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_RI.ioe
inst/extdata/eventsAnnotSample/miso_annotation/RI.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/SE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/MXE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/AFE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/ALE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/TandemUTR.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/A3SS.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/A5SS.hg19.gff3
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.EXSK.Template.2.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MERGE3m.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.IR.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MULTI.Template.2.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MIC.Template.txt
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
