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main(String[]) - Static method in class main_scripts.DICER_main

main(String[]) - Static method in class scripts.ByClassesStandardizer

main(String[]) - Static method in class scripts.CalcDICERStability

main(String[]) - Static method in class scripts.CorrelationsSampler

main(String[]) - Static method in class scripts.DifferentialClusteringSolutionSignificanceEstimator

main(String[]) - Static method in class scripts.DifferentialCorrelationOfClusteringAnalyzer

main(String[]) - Static method in class scripts.GenerateWeightedGraphForCytoscape

main(String[]) - Static method in class scripts.GetMaximumValueInSimMatrix

main(String[]) - Static method in class scripts.GetMetaGraphFromSol

main(String[]) - Static method in class scripts.HyperGeometricEnrichmentAnalysis

main(String[]) - Static method in class scripts.ManyEnrichmentTests

main_scripts - package main_scripts

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

ManyEnrichmentTests - Class in scripts

ManyEnrichmentTests() - Constructor for class scripts.ManyEnrichmentTests

math_utils - package math_utils

MathUtils - Class in math_utils

Misc mathematical functions.

MathUtils() - Constructor for class math_utils.MathUtils

matrix - Variable in class math_utils.ExpressionMatrix

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

unite clusters into median pattern

merge(MetaModule, MetaModule) - Static method in class graph_algorithms.MetaModulePairMerger

mergeLists(HashSet<Integer>, HashSet<Integer>, HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Method in class graph_algorithms.MetaModulePairMerger

meta_modules - Variable in class graph_algorithms.MetaModuleFinder

metaClusters - Variable in class main_scripts.DICER_main

MetaModule - Class in graph_algorithms

MetaModule(HashSet<Integer>, HashSet<Integer>, MetaModuleFinder) - Constructor for class graph_algorithms.MetaModule

MetaModuleFinder - Class in graph_algorithms

MetaModuleFinder(double[][], double[][], ArrayList<String>) - Constructor for class graph_algorithms.MetaModuleFinder

Constructor

MetaModulePairMerger - Class in graph_algorithms

This class implements a simple algorithm that tries to merge two meta-modules.

MetaModulePairMerger() - Constructor for class graph_algorithms.MetaModulePairMerger

MetaModulesMerger - Class in graph_algorithms

This class implements the meta-module merge algorithm.

MetaModulesMerger(Collection<MetaModule>) - Constructor for class graph_algorithms.MetaModulesMerger

MIN_VALS_NUM - Static variable in class EM_LLR_Utils.AbstractParamsEM

modules - Variable in class graph_algorithms.MetaModuleFinder

modules - Variable in class main_scripts.DICER_main