G. Mias Lab »

Index

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__init__() (DataFrame method)

A

addColorbarToFigure() (in module pyiomica.visualizationFunctions)

addVisibilityGraph() (in module pyiomica.visualizationFunctions)

B

BenjaminiHochbergFDR() (in module pyiomica.enrichmentAnalyses)

bootstrapGeneral() (in module pyiomica.frequencySubjectMatch) boxCoxTransform() (DataFrame method)

C

calculateLinksBetweenSubjectsByCorrelation() (in module pyiomica.frequencySubjectMatch) calculateLinksBetweenSubjectsByDistance() (in module pyiomica.frequencySubjectMatch) calculateTimeSeriesCategorization() (in module pyiomica.categorizationFunctions) clusterTimeSeriesCategorization() (in module pyiomica.categorizationFunctions) communityDetectByPathLength() (in module pyiomica.visibilityGraphCommunityDetection) compareTimeSeriesToPoint() (DataFrame method) compareTwoTimeSeries() (DataFrame method)

ConstantGeneDictionary (in module pyiomica.globalVariables) ConstantPyIOmicaDataDirectory (in module pyiomica.globalVariables) ConstantPyIOmicaExamplesDirectory (in module pyiomica.globalVariables) ConstantPyIOmicaExampleVideosDirectory (in module pyiomica.globalVariables) createDirectories() (in module pyiomica.utilityFunctions) createReverseDictionary() (in module pyiomica.utilityFunctions) createVisibilityGraph() (in module pyiomica.visibilityGraphCommunityDetection)

D

DataFrame (class in pyiomica.extendedDataFrame)

E

exportClusteringObject() (in module pyiomica.clusteringFunctions)

ExportEnrichmentReport() (in module pyiomica.enrichmentAnalyses) ExportReactomeEnrichmentReport() (in module pyiomica.enrichmentAnalyses)

F

filterOutAllZeroSignals() (DataFrame method) filterOutFractionMissingSignals() (DataFrame method)

filterOutFractionZeroSignals() (DataFrame method) filterOutReferencePointZeroSignals() (DataFrame method)

G

GeneTranslation() (in module pyiomica.enrichmentAnalyses) getAdjacencyMatrixOfHVG() (in module pyiomica.visibilityGraphAuxiliaryFunctions) getAdjacencyMatrixOfHVGbyNUMPY() (in module pyiomica.visibilityGraphAuxiliaryFunctions) getAdjacencyMatrixOfNVG() (in module pyiomica.visibilityGraphAuxiliaryFunctions) getAdjacencyMatrixOfNVGbyNUMPY() (in module pyiomica.visibilityGraphAuxiliaryFunctions) getCommunitiesOfTimeSeries() (in module pyiomica.clusteringFunctions) getCommunityGenesDict() (in module pyiomica.frequencySubjectMatch) getCommunityStructure() (in module pyiomica.frequencySubjectMatch) getCommunityTopGenesByFrequencyRanking() (in module pyiomica.frequencySubjectMatch) getCommunityTopGenesByNumber() (in module pyiomica.frequencySubjectMatch)

getEstimatedNumberOfClusters() (in module pyiomica.clusteringFunctions) GetGeneDictionary() (in module pyiomica.enrichmentAnalyses) getGroupingIndex() (in module pyiomica.clusteringFunctions) getLombScarglePeriodogramOfDataframe() (in module pyiomica.extendedDataFrame) getNClustersFromLinkageElbow() (in module pyiomica.clusteringFunctions) getNClustersFromLinkageSilhouette() (in module pyiomica.clusteringFunctions) getRandomAutocorrelations() (in module pyiomica.extendedDataFrame) getRandomPeriodograms() (in module pyiomica.extendedDataFrame) getRandomSpikesCutoffs() (in module pyiomica.extendedDataFrame) GOAnalysis() (in module pyiomica.enrichmentAnalyses) GOAnalysisAssigner() (in module pyiomica.enrichmentAnalyses)

I

imputeMissingWithMedian() (DataFrame method)

internalAnalysisFunction() (in module pyiomica.enrichmentAnalyses)

K

KEGGAnalysis() (in module pyiomica.enrichmentAnalyses)

KEGGAnalysisAssigner() (in module pyiomica.enrichmentAnalyses) KEGGDictionary() (in module pyiomica.enrichmentAnalyses)

M

makeClusteringObject() (in module pyiomica.clusteringFunctions) makeDataHistograms() (in module pyiomica.visualizationFunctions) makeDendrogramHeatmapOfClusteringObject() (in module pyiomica.visualizationFunctions) makeLombScarglePeriodograms() (in module pyiomica.visualizationFunctions) makePlotOfPeak() (in module pyiomica.visualizationFunctions) makeVisibilityBarGraph() (in module pyiomica.visualizationFunctions) makeVisibilityGraph() (in module pyiomica.visualizationFunctions) MassDictionary() (in module pyiomica.enrichmentAnalyses) MassMatcher() (in module pyiomica.enrichmentAnalyses) mergeDataframes() (in module pyiomica.extendedDataFrame) modifiedZScore() (DataFrame method)

module pyiomica.categorizationFunctions pyiomica.clusteringFunctions pyiomica.dataStorage pyiomica.enrichmentAnalyses pyiomica.extendedDataFrame pyiomica.frequencySubjectMatch pyiomica.globalVariables pyiomica.utilityFunctions pyiomica.visibilityGraphAuxiliaryFunctions pyiomica.visibilityGraphCommunityDetection pyiomica.visualizationFunctions

N

normalizeSignalsToUnity() (DataFrame method)

O

OBOGODictionary() (in module pyiomica.enrichmentAnalyses)

obtainConstantGeneDictionary() (in module pyiomica.enrichmentAnalyses) optimizeK() (in module pyiomica.frequencySubjectMatch)

P

PackageDirectory (in module pyiomica.globalVariables) plotHVGBarGraphDual() (in module pyiomica.visualizationFunctions) plotNVGBarGraphDual() (in module pyiomica.visualizationFunctions) printPackageGlobalDefaults (in module pyiomica.globalVariables) pyiomica.categorizationFunctions module pyiomica.clusteringFunctions module pyiomica.dataStorage module pyiomica.enrichmentAnalyses module pyiomica.extendedDataFrame module

pyiomica.frequencySubjectMatch module pyiomica.globalVariables module pyiomica.utilityFunctions module pyiomica.visibilityGraphAuxiliaryFunctions module pyiomica.visibilityGraphCommunityDetection module pyiomica.visualizationFunctions module

Q

quantileNormalize() (DataFrame method)

R

ReactomeAnalysis() (in module pyiomica.enrichmentAnalyses) read() (in module pyiomica.dataStorage) readMathIOmicaData() (in module pyiomica.utilityFunctions)

removeConstantSignals() (DataFrame method) runCPUs() (in module pyiomica.utilityFunctions) runForClusterNum() (in module pyiomica.clusteringFunctions)

S

saveFigure() (in module pyiomica.visualizationFunctions)

splitGenes() (in module pyiomica.frequencySubjectMatch)

T

tagLowValues() (DataFrame method)

tagMissingAsValue() (DataFrame method) tagValueAsMissing() (DataFrame method)

V

visualizeTimeSeriesCategorization() (in module pyiomica.categorizationFunctions)

W

write() (in module pyiomica.dataStorage)