psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
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API

API for psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Global functions
.onAttach Man page Source code
ASquantFileInput Man page Source code
HTMLfast Man page Source code
SraRunTableSampleInfoFormat Source code
[.GEandAScorrelation Man page
[.sticky Man page
`[.GEandAScorrelation` Source code
`[.sticky` Source code
addFileAttrs Source code
addObjectAttrs Man page
addTCGAdata Man page Source code
analysesPlotSet Man page Source code
analysesServer Man page Source code
analysesTableSet Man page Source code
analysesUI Man page Source code
appServer Man page Source code
appUI Man page Source code
appendNewGroups Man page Source code
areSplicingEvents Man page Source code
articleUI Man page Source code
as.table.GEandAScorrelation Man page
assignColours Man page Source code
assignValuePerPatient Man page
assignValuePerSubject Man page Source code
basicStats Man page Source code
blendColours Man page
browserHistory Man page Source code
calculateAxisStats Source code
calculateInclusionLevels Man page Source code
calculateLoadingsContribution Man page Source code
checkFileFormat Man page Source code
checkFirebrowse Man page Source code
checkGroupType Man page Source code
checkIntegrity Man page Source code
checkSurvivalInput Man page
chooseFilesLinux Source code
chooseFilesMac Source code
closeProgress Man page Source code
clusterICAset Man page Source code
clusterSet Man page Source code
colSums,EList-method Man page
collapseElemsToSingleString Source code
colourInputMod Man page Source code
colsAsNumbers Source code
combineSplicingEventInfo Source code
contextUI Source code
convertGeneIdentifiers Man page Source code
convertListOfLists2DataFrame Source code
convertNumberCols2Numbers Source code
correlateGEandAS Man page Source code
correlationServer Man page Source code
correlationUI Man page Source code
createDataTab Man page Source code
createDensitySparklines Man page Source code
createEventPlotting Man page Source code
createGroup Man page Source code
createGroupByAttribute Man page Source code
createGroupById Man page Source code
createGroupFromInput Man page Source code
createJunctionsTemplate Man page Source code
createOptimalSurvData Man page Source code
createSparklines Man page Source code
customColMedians Man page Source code
customRowMaxs Man page Source code
customRowMeans Man page Source code
customRowMedians Man page Source code
customRowMins Man page Source code
customRowRanges Man page Source code
customRowVars Man page Source code
dataServer Man page Source code
dataUI Man page Source code
diagramSplicingEvent Man page Source code
diffAnalyses Man page Source code
diffExpressionEventServer Man page Source code
diffExpressionEventUI Man page Source code
diffExpressionServer Man page Source code
diffExpressionSet Man page Source code
diffExpressionTableServer Man page Source code
diffExpressionTableUI Man page Source code
diffExpressionUI Man page Source code
diffSplicingEventServer Man page Source code
diffSplicingEventUI Man page Source code
diffSplicingServer Man page Source code
diffSplicingSet Man page Source code
diffSplicingTableServer Man page Source code
diffSplicingTableUI Man page Source code
diffSplicingUI Man page Source code
dimReductionServer Man page Source code
dimReductionUI Man page Source code
disableTab Man page Source code
discardElemsInList Source code
discardLowCoveragePSIvalues Man page Source code
discardOutsideSamplesFromGroups Man page Source code
display Man page Source code
downloadFiles Man page Source code
downloadGtexFiles Source code
downloadRecountData Source code
drawCurve Source code
drawPath Source code
drawRect Source code
drawText Source code
enableTab Man page Source code
endProcess Man page Source code
ensemblToUniprot Man page Source code
errorAlert Man page Source code
errorDialog Man page Source code
errorModal Man page Source code
escape Man page Source code
eventPlotOptions Man page Source code
exportGroupsToFile Man page Source code
export_highcharts Man page Source code
fasterDataStats Source code
fileBrowser Man page Source code
fileBrowserInput Man page Source code
filterGeneExpr Man page Source code
filterGroups Man page Source code
filterPSI Man page Source code
findASeventsFromGene Man page Source code
findEventData Man page Source code
firebrowseGeneExpressionFormat Source code
firebrowseJunctionReadsFormat Source code
firebrowseMergeClinicalFormat Source code
firebrowseNormalizedGeneExpressionFormat Source code
firebrowseServer Man page Source code
firebrowseUI Man page Source code
fisher Man page Source code
fligner Man page Source code
geNormalisationFilteringInterface Man page Source code
geNormalisationFilteringServer Man page Source code
geNormalisationFilteringUI Man page Source code
geneExprFileInput Man page Source code
geneExprFilteringSetting Source code
geneExprSurvSet Man page Source code
genericClinicalFormat Source code
genericGeneExpressionFormat Source code
genericInclusionLevelsFormat Source code
genericJunctionReadsFormat Source code
genericSampleInfoFormat Source code
getASevent Man page
getASevents Man page
getActiveDataset Man page
getAnnotationName Man page Source code
getAssemblyVersion Man page Source code
getAttributesTime Man page Source code
getAutoNavigation Man page
getCategories Man page
getCategory Man page
getCategoryData Man page
getClinicalData Man page Source code
getClinicalDataForSurvival Man page Source code
getClinicalMatchFrom Man page Source code
getCognateGenesToFilter Source code
getCoordPosByEventType Source code
getCores Man page
getCorrelation Man page Source code
getData Man page
getDataRows Man page Source code
getDifferentialExpression Man page Source code
getDifferentialExpressionColumns Man page Source code
getDifferentialExpressionFiltered Man page Source code
getDifferentialExpressionResetPaging Man page Source code
getDifferentialExpressionSurvival Man page Source code
getDifferentialSplicing Man page Source code
getDifferentialSplicingColumns Man page Source code
getDifferentialSplicingFiltered Man page Source code
getDifferentialSplicingResetPaging Man page Source code
getDifferentialSplicingSurvival Man page Source code
getDownloadsFolder Man page Source code
getEvent Man page
getFirebrowseCohorts Man page
getFirebrowseDataTypes Man page
getFirebrowseDateFormat Man page Source code
getFirebrowseDates Man page
getGeneExpression Man page Source code
getGeneList Man page Source code
getGenes Man page
getGenesFromSplicingEvents Man page Source code
getGlobal Man page Source code
getGroupIndependenceTesting Man page Source code
getGroups Man page Source code
getGtexDataTypes Man page Source code
getGtexDataURL Man page Source code
getGtexReleases Man page Source code
getGtexTissues Man page Source code
getHidden Man page Source code
getHighlightedPoints Man page Source code
getICA Man page Source code
getInclusionLevels Man page
getInclusionLevelsSummaryStatsCache Man page Source code
getJunctionQuantification Man page Source code
getLabelledPoints Man page Source code
getMatchingSamples Man page
getNumerics Man page Source code
getPCA Man page Source code
getPSIsummaryStats Source code
getPatientFromSample Man page
getPrecision Man page Source code
getSampleAttributes Man page Source code
getSampleFromPatient Man page
getSampleFromSubject Man page Source code
getSampleId Man page
getSampleInfo Man page
getSelectedGroups Man page Source code
getSelectedPoints Man page Source code
getServerFunctions Man page Source code
getSignificant Man page Source code
getSpecies Man page Source code
getSplicingEventCoordinates Man page Source code
getSplicingEventData Man page Source code
getSplicingEventFromGenes Man page Source code
getSplicingEventTypes Man page Source code
getSubjectAttributes Man page Source code
getSubjectFromSample Man page Source code
getSubjectId Man page Source code
getTCGAcohorts Man page Source code
getTCGAdataTypes Man page Source code
getTCGAdates Man page Source code
getURLtoDownload Man page Source code
getUiFunctions Man page Source code
getValidEvents Man page Source code
getValuePerPatient Man page
getValuePerSubject Man page
getZoom Man page Source code
ggplotAuxServer Man page Source code
ggplotServer Man page Source code
ggplotTooltip Man page Source code
ggplotUI Man page Source code
globalSelectize Man page Source code
groupByAttribute Man page Source code
groupByExpression Man page Source code
groupByGrep Man page Source code
groupById Man page Source code
groupByPreMadeList Man page Source code
groupManipulation Man page Source code
groupManipulationInput Man page Source code
groupPerElem Man page Source code
groupsServer Man page Source code
groupsServerOnce Man page Source code
groupsUI Man page Source code
gtexClinicalInfoFormat Source code
gtexDataServer Man page Source code
gtexDataUI Man page Source code
gtexGeneReadsFormat Source code
gtexJunctionReadsFormat Source code
gtexSampleInfoFormat Source code
gtexV7ClinicalInfoFormat Source code
gtexV7JunctionReadsFormat Source code
gtexV8JunctionReadsFormat Source code
hc_scatter Man page
hchart.survfit Man page Source code
helpServer Man page Source code
helpUI Man page Source code
icaServer Man page Source code
icaUI Man page Source code
importGroupsFrom Man page Source code
inclusionLevelsFilterInterface Man page Source code
inclusionLevelsFilterServer Man page Source code
inclusionLevelsFilterUI Man page Source code
inclusionLevelsInterface Man page Source code
inclusionLevelsServer Man page Source code
inclusionLevelsUI Man page Source code
infoModal Man page Source code
infoServer Man page Source code
infoUI Man page Source code
inheritAttrs Source code
initialiseEventData Source code
inlineDialog Man page Source code
insideFile Man page Source code
is.whole Man page Source code
isFile Man page Source code
isFirebrowseUp Man page Source code
isRStudioServer Man page Source code
joinEventsPerType Man page Source code
junctionString Man page Source code
kruskal Man page Source code
labelBasedOnCutoff Man page
levene Man page Source code
leveneTest Man page Source code
linkToArticles Man page Source code
linkToRunJS Man page Source code
listAllAnnotations Man page Source code
listPairs Source code
listSplicingAnnotations Man page Source code
loadAnnotation Man page Source code
loadBy Man page Source code
loadCustomSplicingAnnotationSet Man page Source code
loadFile Man page Source code
loadFileFormats Man page Source code
loadFirebrowseData Man page
loadFirebrowseFolders Man page Source code
loadGeneExpressionSet Man page Source code
loadGtexData Man page Source code
loadGtexDataShiny Man page Source code
loadGtexFile Man page Source code
loadLocalFiles Man page Source code
loadRecountGeneExpression Source code
loadRecountJunctionQuant Source code
loadRequiredData Man page Source code
loadSRAproject Man page Source code
loadSplicingQuantificationSet Man page Source code
loadTCGAdata Man page Source code
loadTCGAsampleMetadata Man page Source code
loadedDataModal Man page Source code
localDataServer Man page Source code
localDataUI Man page Source code
matchGroupASeventsAndGenes Man page Source code
matchGroupSubjectsAndSamples Man page Source code
matchSplicingEventsWithGenes Man page Source code
missingDataGuide Man page Source code
missingDataModal Man page Source code
modTabPanel Man page Source code
navSelectize Man page Source code
normaliseGeneExpression Man page Source code
normalizeGeneExpression Man page
numericInputWithCheckbox Source code
operateOnGroups Man page Source code
optimSurvDiffSet Man page Source code
optimalSurvivalCutoff Man page Source code
parseCategoricalGroups Man page Source code
parseDateResponse Man page Source code
parseEventData Source code
parseEventFromStr Source code
parseFile Man page Source code
parseFirebrowseMetadata Man page Source code
parseMatsA3SS Man page Source code
parseMatsA5SS Man page Source code
parseMatsAFE Man page Source code
parseMatsALE Man page Source code
parseMatsAnnotation Man page Source code
parseMatsEvent Man page Source code
parseMatsGeneric Man page Source code
parseMatsMXE Man page Source code
parseMatsRI Man page Source code
parseMatsSE Man page Source code
parseMisoA3SS Man page Source code
parseMisoA5SS Man page Source code
parseMisoAFE Man page Source code
parseMisoALE Man page Source code
parseMisoAnnotation Man page Source code
parseMisoEvent Man page Source code
parseMisoEventID Man page Source code
parseMisoGeneric Man page Source code
parseMisoId Man page Source code
parseMisoMXE Man page Source code
parseMisoRI Man page Source code
parseMisoSE Man page Source code
parseMisoTandemUTR Man page Source code
parseSampleGroups Man page
parseSpeciesAssembly Source code
parseSplicingEvent Man page Source code
parseSuppaA3SS Man page
parseSuppaA5SS Man page
parseSuppaAFE Man page
parseSuppaALE Man page
parseSuppaAnnotation Man page Source code
parseSuppaEvent Man page Source code
parseSuppaGeneric Man page Source code
parseSuppaMXE Man page
parseSuppaRI Man page
parseSuppaSE Man page
parseTCGAsampleInfo Man page Source code
parseTCGAsampleTypes Man page Source code
parseTcgaSampleInfo Man page
parseUniprotXML Man page Source code
parseUrlsFromFirebrowseResponse Man page Source code
parseVastToolsA3SS Man page
parseVastToolsA5SS Man page
parseVastToolsAnnotation Man page Source code
parseVastToolsEvent Man page Source code
parseVastToolsRI Man page
parseVastToolsSE Man page
pcaServer Man page Source code
pcaUI Man page Source code
performICA Man page Source code
performPCA Man page Source code
performSimpleDiffExpr Source code
plot.GEandAScorrelation Man page Source code
plotASeventRegion Source code
plotClusters Man page Source code
plotCorrelation Man page
plotDistribution Man page Source code
plotGeneExprPerSample Man page Source code
plotGroupIndependence Man page Source code
plotICA Man page Source code
plotLibrarySize Man page Source code
plotPCA Man page Source code
plotPCAvariance Man page Source code
plotPointsStyle Man page Source code
plotProtein Man page Source code
plotRowStats Man page Source code
plotSingleICA Man page Source code
plotSplicingEvent Man page Source code
plotSplicingEventHelper Source code
plotSurvivalCurves Man page Source code
plotSurvivalPvaluesByCutoff Man page Source code
plotTranscripts Man page Source code
plotVariance Man page
plottableXranges Man page Source code
prepareAnnotationFromEvents Man page Source code
prepareDatatablePlots Source code
prepareDatatableSettingsTable Source code
prepareEventInfoTooltip Source code
prepareEventPlotOptions Man page Source code
prepareExternalLinks Source code
prepareFileBrowser Man page Source code
prepareFirebrowseArchives Man page Source code
prepareGenePresentation Man page Source code
prepareGeneQuant Man page Source code
prepareGeneQuantSTAR Man page Source code
prepareJunctionQuant Man page Source code
prepareJunctionQuantSTAR Man page Source code
preparePreMadeGroupForSelection Man page Source code
prepareSRAmetadata Man page Source code
prepareSVG Source code
prepareWordBreak Man page Source code
preserveAttributes Man page Source code
prettifyEventID Source code
prettifyEventType Source code
print.GEandAScorrelation Man page Source code
print.geneList Source code
print.splicingEventPlot Source code
print.splicingEventPlotList Source code
processButton Man page Source code
processClickRedirection Man page Source code
processCol Source code
processDatasetNames Man page Source code
processEventDataByType Source code
processSRAdata Man page Source code
processSurvData Man page Source code
processSurvTerms Man page Source code
processSurvival Man page Source code
processVastToolsPSItable Source code
psiFastCalc Source code
psiFastCalc2 Source code
psiFilteringSet Source code
psiFilteringSetting Source code
psichomics Man page Source code
psichomicsGeneExpressionFormat Source code
psichomicsInclusionLevelsFormat Source code
pubmedUI Man page Source code
quantifySplicing Man page Source code
quantifySplicingSet Man page Source code
queryEnsembl Man page Source code
queryEnsemblByEvent Man page Source code
queryEnsemblByGene Man page Source code
queryFirebrowseData Man page Source code
queryPubMed Man page Source code
queryUniprot Man page Source code
readAnnot Man page Source code
readFile Man page Source code
recountDataServer Man page Source code
recountDataUI Man page Source code
recountSampleFormat Source code
reduceDimensionality Man page Source code
removeAlert Man page Source code
removeRedundantDatasets Source code
renameDuplicated Man page Source code
renameGroups Man page Source code
renderBoxplot Man page Source code
renderDataTableSparklines Man page Source code
renderGeneticInfo Man page Source code
renderGroupInterface Man page Source code
renderProteinInfo Man page Source code
rm.null Man page Source code
roundDigits Man page Source code
roundMaxUp Man page Source code
roundMinDown Man page Source code
saveProcessedSRAdata Man page Source code
selectGroupsServer Man page Source code
selectGroupsUI Man page
selectPreMadeGroup Man page Source code
selectizeGeneInput Man page Source code
setASevent Man page Source code
setActiveDataset Man page Source code
setAnnotationName Man page Source code
setAssemblyVersion Man page Source code
setAutoNavigation Man page Source code
setCategory Man page Source code
setClinicalMatchFrom Man page Source code
setCores Man page Source code
setCorrelation Man page Source code
setData Man page Source code
setDataTable Man page Source code
setDifferentialExpression Man page Source code
setDifferentialExpressionColumns Man page Source code
setDifferentialExpressionFiltered Man page Source code
setDifferentialExpressionResetPaging Man page Source code
setDifferentialExpressionSurvival Man page Source code
setDifferentialSplicing Man page Source code
setDifferentialSplicingColumns Man page Source code
setDifferentialSplicingFiltered Man page Source code
setDifferentialSplicingResetPaging Man page Source code
setDifferentialSplicingSurvival Man page Source code
setEvent Man page
setFirebrowseData Man page Source code
setGlobal Man page Source code
setGroupIndependenceTesting Man page Source code
setGroups Man page Source code
setHidden Man page Source code
setHighlightedPoints Man page Source code
setICA Man page Source code
setInclusionLevels Man page Source code
setInclusionLevelsSummaryStatsCache Man page Source code
setLabelledPoints Man page Source code
setLocalData Man page Source code
setMultipleFilesData Man page Source code
setNormalisedGeneExpression Man page Source code
setOperation Man page Source code
setOperationIcon Man page
setPCA Man page Source code
setPrecision Man page Source code
setSampleInfo Man page Source code
setSelectedPoints Man page Source code
setSignificant Man page Source code
setSpecies Man page Source code
setURLtoDownload Man page Source code
setZoom Man page Source code
showAlert Man page Source code
showGroupsTable Man page Source code
sidebar Man page Source code
signifDigits Man page Source code
singleDiffAnalyses Man page Source code
sortCoordinates Man page Source code
spearman Man page Source code
startProcess Man page Source code
startProgress Man page Source code
styleModal Man page Source code
subjectMultiMatchWarning Man page Source code
subsetGeneExpressionFromMatchingGenes Man page Source code
successAlert Man page Source code
survdiffTerms Man page Source code
survfit.survTerms Man page Source code
survivalServer Man page Source code
survivalUI Man page Source code
t.sticky Man page Source code
tabDataset Man page Source code
table2html Man page Source code
tableRow Man page
templateServer Man page Source code
templateUI Man page Source code
testGroupIndependence Man page Source code
testSingleIndependence Man page Source code
testSurvival Man page
testSurvivalCutoff Man page Source code
textSuggestions Man page Source code
toJSarray Man page Source code
transformData Man page Source code
transformOptions Man page Source code
transformValues Man page Source code
trimWhitespace Man page Source code
ttest Man page Source code
uniqueBy Man page Source code
updateClinicalParams Man page Source code
updateFileBrowserInput Man page Source code
updateProgress Man page Source code
vasttoolsGeneExpressionFormat Source code
vasttoolsInclusionLevelsFormat Source code
vasttoolsInclusionLevelsTidyFormat Source code
vennEvents Man page Source code
warningAlert Man page Source code
warningDialog Man page Source code
warningModal Man page Source code
wilcox Man page Source code
writeLengthWithinRect Source code
psichomics documentation built on Nov. 8, 2020, 5:44 p.m.

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