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

Global functions
ASquantFileInput Man page Source code
addTCGAdata Man page Source code
analysesServer Man page Source code
analysesUI Man page Source code
appServer Man page Source code
appUI Man page Source code
appendNewGroups Man page Source code
articleUI Man page Source code
assignColours Man page Source code
basicStats Man page Source code
blendColours Man page Source code
browserHistory Man page Source code
bsModal2 Man page Source code
calculateInclusionLevels Man page Source code
checkFileFormat Man page Source code
checkFirebrowse Man page Source code
checkIntegrity Man page Source code
checkSurvivalInput Man page Source code
closeProgress Man page Source code
clusterICAset Man page Source code
clusterSet Man page Source code
colsAsNumbers 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
createGroupByColumn 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
dataServer Man page Source code
dataUI Man page Source code
diffAnalyses Man page Source code
diffAnalysesPlotSet Man page Source code
diffAnalysesSet Man page Source code
diffAnalysesTableSet Man page Source code
diffExpressionEventServer Man page Source code
diffExpressionEventUI Man page Source code
diffExpressionPlotSet Man page Source code
diffExpressionServer Man page Source code
diffExpressionSet Man page Source code
diffExpressionTableServer Man page Source code
diffExpressionTableSet 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
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
display Man page Source code
downloadFiles Man page 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
export_highcharts Man page Source code
fileBrowser Man page Source code
fileBrowserInput Man page Source code
filterGroups 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
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 Source code
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
getColumnsTime Man page Source code
getCores Man page
getData Man page
getDataRows Man page Source code
getDifferentialAnalyses Man page Source code
getDifferentialAnalysesColumns Man page Source code
getDifferentialAnalysesFiltered Man page Source code
getDifferentialAnalysesResetPaging Man page Source code
getDifferentialAnalysesSurvival Man page Source code
getDifferentialExpression Man page Source code
getDifferentialExpressionColumns Man page Source code
getDifferentialExpressionFiltered Man page Source code
getDifferentialExpressionResetPaging Man page Source code
getDownloadsFolder Man page Source code
getEvent Man page
getFirebrowseCohorts Man page Source code
getFirebrowseDataTypes Man page Source code
getFirebrowseDateFormat Man page Source code
getFirebrowseDates Man page Source code
getFirehoseCohorts Man page
getFirehoseDataTypes Man page
getFirehoseDates Man page
getGTExTissues Man page
getGeneExpression Man page Source code
getGenes Man page Source code
getGenesFromSplicingEvents Man page Source code
getGlobal Man page Source code
getGroupIndependenceTesting Man page Source code
getGroups 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
getJunctionQuantification Man page Source code
getLabelledPoints Man page Source code
getMatchingSamples Man page Source code
getNumerics Man page Source code
getPCA Man page Source code
getPSIperPatient Man page Source code
getPatientAttributes Man page Source code
getPatientFromSample Man page Source code
getPatientId Man page Source code
getPrecision Man page
getSampleAttributes Man page Source code
getSampleId Man page Source code
getSampleInfo Man page
getSelectedGroups Man page Source code
getSelectedPoints Man page Source code
getServerFunctions Man page Source code
getSignificant Man page
getSpecies Man page Source code
getSplicingEventCoordinates Man page Source code
getSplicingEventFromGenes Man page Source code
getSplicingEventTypes Man page Source code
getTCGAcohorts Man page
getTCGAdates Man page
getURLtoDownload Man page Source code
getUiFunctions Man page Source code
getValidEvents Man page Source code
getValuePerPatient Man page Source code
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
groupManipulation Man page Source code
groupManipulationInput Man page Source code
groupPerElem Man page Source code
groupPerPatient Man page Source code
groupPerSample 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
hc_scatter Man page Source code
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
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
inlineDialog Man page Source code
insideFile Man page Source code
is.whole Man page Source code
isFirebrowseUp Man page Source code
isFirehoseUp Man page
joinEventsPerType Man page Source code
junctionString Man page Source code
kruskal Man page Source code
labelBasedOnCutoff Man page Source code
levene Man page Source code
leveneTest Man page Source code
listAllAnnotations Man page 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 Source code
loadFirebrowseFolders Man page Source code
loadFirehoseData Man page
loadFirehoseFolders Man page
loadGTExFile Man page
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
loadRequiredData Man page Source code
loadSplicingQuantificationSet Man page Source code
loadTCGAdata Man page
loadTCGAfolders Man page
loadTCGAsampleMetadata Man page Source code
loadedDataModal Man page Source code
localDataServer Man page Source code
localDataUI Man page Source code
matchPatientToSingleSample 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
noinfo Man page Source code
normaliseGeneExpression Man page Source code
onAttach Source code
operateOnGroups Man page Source code
optimSurvDiffSet Man page Source code
optimalPSIcutoff Man page Source code
parseCategoricalGroups Man page Source code
parseDateResponse Man page Source code
parseFirebrowseMetadata Man page Source code
parseFirehoseMetadata Man page
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 Source code
parseSplicingEvent Man page Source code
parseSuppaA3SS Man page Source code
parseSuppaA5SS Man page Source code
parseSuppaAFE Man page Source code
parseSuppaALE Man page Source code
parseSuppaAnnotation Man page Source code
parseSuppaEvent Man page Source code
parseSuppaGeneric Man page Source code
parseSuppaMXE Man page Source code
parseSuppaRI Man page Source code
parseSuppaSE Man page Source code
parseTCGAmetadata Man page
parseTcgaSampleInfo Man page Source code
parseUniprotXML Man page Source code
parseUrlsFromFirebrowseResponse Man page Source code
parseUrlsFromFirehoseResponse Man page
parseValidFile Man page Source code
parseVastToolsA3SS Man page Source code
parseVastToolsA5SS Man page Source code
parseVastToolsAnnotation Man page Source code
parseVastToolsEvent Man page Source code
parseVastToolsRI Man page Source code
parseVastToolsSE Man page Source code
pcaServer Man page Source code
pcaUI Man page Source code
performICA Man page Source code
performPCA Man page Source code
plotClusters Man page Source code
plotCorrelation Man page Source code
plotDistribution Man page Source code
plotGroupIndependence Man page Source code
plotICA Man page Source code
plotPCA Man page Source code
plotPointsStyle Man page Source code
plotProtein Man page Source code
plotSingleICA Man page Source code
plotSurvivalCurves Man page Source code
plotTranscripts Man page Source code
plotVariance Man page Source code
plottableXranges Man page Source code
prepareAnnotationFromEvents Man page Source code
prepareEventPlotOptions Man page Source code
prepareFileBrowser Man page Source code
prepareFirebrowseArchives Man page Source code
prepareFirehoseArchives Man page
prepareTCGAarchives Man page
processButton Man page Source code
processDatasetNames Man page Source code
processSurvData Man page Source code
processSurvTerms Man page Source code
processSurvival Man page 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
queryFirehoseData Man page
queryPubMed Man page Source code
queryUniprot Man page Source code
readAnnot Man page Source code
readFile Man page Source code
reduceDimensionality Man page Source code
removeAlert Man page Source code
renameDuplicated Man page Source code
renameGroups 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
rowMeans Man page Source code
rowVars Man page Source code
selectGroupsServer Man page Source code
selectGroupsUI 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
setData Man page Source code
setDataTable Man page Source code
setDifferentialAnalyses Man page Source code
setDifferentialAnalysesColumns Man page Source code
setDifferentialAnalysesFiltered Man page Source code
setDifferentialAnalysesResetPaging Man page Source code
setDifferentialAnalysesSurvival Man page Source code
setDifferentialExpression Man page Source code
setDifferentialExpressionColumns Man page Source code
setDifferentialExpressionFiltered Man page Source code
setDifferentialExpressionResetPaging 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
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 Source code
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
survdiff.survTerms Man page Source code
survfit.survTerms Man page Source code
survivalServer Man page Source code
survivalUI Man page Source code
tabDataset Man page Source code
table2html Man page Source code
tableRow Man page Source code
templateServer Man page Source code
templateUI Man page Source code
testGroupIndependence Man page Source code
testSingleIndependence Man page Source code
testSurvival Man page Source code
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
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
nuno-agostinho/psichomics documentation built on Nov. 1, 2017, 3:18 p.m.