A B C D E F G H I K L M O P R S T U V W _

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gammln(double) - Static method in class math_utils.HelperFuncs

Returns the value ln(Gamma(xx)) for xx>0.

gammp(double, double) - Static method in class math_utils.HelperFuncs

Returns the incomplete gamma function P(a,x).

gammq(double, double) - Static method in class math_utils.HelperFuncs

Returns the incomplete gamma function Q(a,x)=1-P(a,x).

gcf(double, double) - Static method in class math_utils.HelperFuncs

Returns the incomplete gamma function Q(a,x) evaluated by its continued fraction representation.

geneGenesCorrelations(String, String) - Method in class math_utils.ExpressionMatrix

geneNames - Variable in class graph_algorithms.MetaModuleFinder

generateAllPairsSeeds(int, float, float, int) - Method in class EM_LLR_Utils.SeedGenerator

generateAllPairsSeedsWithConfinedCut(int, float, float, int, double, Map<Interaction, Double>) - Method in class EM_LLR_Utils.SeedGenerator

GenerateWeightedGraphForCytoscape - Class in scripts

This script is for creating sif files for analysis in cytoscape.

GenerateWeightedGraphForCytoscape() - Constructor for class scripts.GenerateWeightedGraphForCytoscape

genesID - Variable in class math_utils.ExpressionMatrix

getBetweenAvgDCScores(HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Static method in class graph_algorithms.MetaModulePairMerger

getBetweenAvgGCScores(HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Static method in class graph_algorithms.MetaModulePairMerger

getBetweenDCScores(HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Static method in class graph_algorithms.MetaModulePairMerger

getBetweenGCScores(HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Static method in class graph_algorithms.MetaModulePairMerger

A set of auxiliary static methods

getBetweenScores(HashSet<Integer>, HashSet<Integer>, double[][]) - Static method in class graph_algorithms.MetaModulePairMerger

getCDFofBinomialDist(int, int, float) - Static method in class math_utils.staticMathHelperMethods

getClassesBorders() - Method in class main_scripts.TscoresCalculator

getClickWeightedMatrix(boolean) - Method in class EM_LLR_Utils.LLRScoresCalculator

getConsistentCorrelationsGraph() - Method in class main_scripts.DCGraphsCalculator

getDCGraphs() - Method in class main_scripts.DCGraphsCalculator

getDoubleTrasposedMatrix() - Method in class math_utils.ExpressionMatrix

getDownClusterer() - Method in class main_scripts.DICER_main

getEdgesForAlgo(double) - Method in class graph_algorithms.MetaModuleFinder

getEnrichedTerms() - Method in class scripts.HyperGeometricEnrichmentAnalysis

getExpandedByGraph(short[][]) - Method in class math_utils.ExpressionMatrix

getFinalSolution(int, int) - Method in class graph_algorithms.MetaModuleFinder

getGenesID() - Method in class math_utils.ExpressionMatrix

getHeader() - Method in class math_utils.ExpressionMatrix

getHyperGeometricPval(int, int, int, int) - Static method in class math_utils.staticMathHelperMethods

getHyperGeometricPvalEstimates(int, int, int, int) - Static method in class math_utils.staticMathHelperMethods

getId2Index() - Method in class math_utils.SimilarityMatrix

getJaccardScore(Collection<String>, Collection<String>) - Static method in class scripts.CalcDICERStability

getJaccardScore(boolean[][], boolean[][]) - Static method in class scripts.CalcDICERStability

getLikelihood() - Method in class EM_LLR_Utils.AbstractParamsEM

getMatesDistribution() - Method in class EM_LLR_Utils.AbstractParamsEM

getMatesP() - Method in class EM_LLR_Utils.AbstractParamsEM

getMatrix() - Method in class math_utils.ExpressionMatrix

getMatrixDeepClone(float[][]) - Static method in class math_utils.staticMathHelperMethods

getMaximalSupervisedSimilairtyROCScore(float[], float[], int[], int[], Random) - Static method in class math_utils.staticMathHelperMethods

getMaximalSupervisedSimilairtyTScore(float[], float[], int[], int[], Random) - Static method in class math_utils.staticMathHelperMethods

GetMaximumValueInSimMatrix - Class in scripts

GetMaximumValueInSimMatrix() - Constructor for class scripts.GetMaximumValueInSimMatrix

getMeanMatesLikelihood() - Method in class EM_LLR_Utils.LLRScoresCalculator

getMetaClusters() - Method in class main_scripts.DICER_main

getMetaGraph() - Method in class main_scripts.DICER_main

getMetaGraph(LinkedList<HashSet<Integer>>) - Method in class main_scripts.DICER_main

GetMetaGraphFromSol - Class in scripts

This script calculates the "meta-file" of a clustering solution.

GetMetaGraphFromSol() - Constructor for class scripts.GetMetaGraphFromSol

getMetaModules() - Method in class graph_algorithms.MetaModulesMerger

getMetaModules() - Method in class graph_algorithms.SingletonsAndMetaModulesMerger

getMetaModules(String, MetaModuleFinder, Hashtable<String, HashSet<String>>) - Static method in class main_scripts.DICER_main

getModules(MetaModuleFinder, String, Hashtable<String, HashSet<String>>) - Static method in class main_scripts.DICER_main

getModules() - Method in class main_scripts.DICER_main

getModulesList() - Method in class graph_algorithms.MetaModulesMerger

getModulesList() - Method in class graph_algorithms.SingletonsAndMetaModulesMerger

getNonMatesDistribution() - Method in class EM_LLR_Utils.AbstractParamsEM

getSampleVec(int, MatrixData) - Static method in class math_utils.PercentileCalc

getSetAsArrayList(TscoresCalculator, Collection<String>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

getShuffeledCorrelationEstimates(float[][], String, int, Random, int, int) - Static method in class math_utils.staticMathHelperMethods

getShuffeledMatrixByColumns(Random) - Method in class math_utils.ExpressionMatrix

getSimilarities() - Method in class math_utils.SimilarityMatrix

getSimilarity(String, String) - Method in class math_utils.SimilarityMatrix

getSimilarity(int, int) - Method in class math_utils.SimilarityMatrix

getSimLikeLihood(double, boolean) - Method in class EM_LLR_Utils.LLRScoresCalculator

getSortedRealScoresSample(float[][], float, String, int, int, boolean) - Static method in class math_utils.staticMathHelperMethods

getSortedRealScoresSample(float[][], float, String, boolean) - Static method in class math_utils.staticMathHelperMethods

getSubMatrixByColumnsIndices(ArrayList<Integer>) - Method in class math_utils.ExpressionMatrix

This method receives a sorted list of indices and returns a sub-matrix that contains only the columns that are included in the list

getSubMatrixByRowsIndices(LinkedList<Integer>) - Method in class math_utils.ExpressionMatrix

This method returns a sub-matrix with all the raws that appear in the list.

getSumOfScores(TscoresCalculator, Collection<String>) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

getSumOfScores(TscoresCalculator, HashSet<String>, HashSet<String>, boolean) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

getTtestPval(float[], int, int) - Static method in class math_utils.staticMathHelperMethods

getTtestPval(double[], double[]) - Static method in class math_utils.staticMathHelperMethods

getUnion() - Method in class graph_algorithms.MetaModule

getUpCorrelatedClusters() - Method in class main_scripts.DICER_main

getWeightedMatrix() - Method in class EM_LLR_Utils.LLRScoresCalculator

getWithinSetScores(Collection<Integer>) - Method in class graph_algorithms.MetaModuleFinder

globalCorrelationsLLRAnalyzer - Variable in class main_scripts.DCGraphsCalculator

globalCorrelationsLLRAnalyzer - Variable in class main_scripts.DICER_main

graph_algorithms - package graph_algorithms

greedyRemoveNodesFromTwoSides(Collection<Integer>, Collection<Integer>) - Method in class graph_algorithms.MetaModuleFinder

This methods receives as input two distinct sets.

gser(double, double) - Static method in class math_utils.HelperFuncs

Returns the incomplete gamma function P(a,x) evaluated by its series representation.