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

S

scoredTscoresGraph - Variable in class main_scripts.TscoresCalculator

scripts - package scripts

SeedGenerator<T extends edu.tau.compbio.interaction.AnnotatedInteractorSet> - Class in EM_LLR_Utils

SeedGenerator(InteractionMap, SimilarityMatrix, int[], SeedGenerator.SeedScore, SeedGenerator.SeedConfinement) - Constructor for class EM_LLR_Utils.SeedGenerator

SeedGenerator.BestNeiSelection - Enum in EM_LLR_Utils

SeedGenerator.SeedConfinement - Enum in EM_LLR_Utils

SeedGenerator.SeedScore - Enum in EM_LLR_Utils

setBestNeiSelectionMethod(SeedGenerator.BestNeiSelection) - Method in class EM_LLR_Utils.SeedGenerator

setDistributions(NormalDistribution, NormalDistribution, double) - Method in class EM_LLR_Utils.LLRScoresCalculator

setGlobalGraphForOneClass(int) - Method in class main_scripts.TscoresCalculator

setInit(boolean) - Method in class EM_LLR_Utils.RegParamsEM

setInitial(NormalDistribution, NormalDistribution, double) - Method in class EM_LLR_Utils.RegParamsEM

setK(double) - Method in class main_scripts.DCGraphsCalculator

setLikelihoodThresholdForDC(float) - Method in class graph_algorithms.MetaModuleFinder

setMatesMaxP(float) - Method in class EM_LLR_Utils.LLRScoresCalculator

setMatrix(float[][]) - Method in class math_utils.ExpressionMatrix

setPMatesRange(float, float) - Method in class EM_LLR_Utils.RegParamsEM

setSameStd(boolean) - Method in class EM_LLR_Utils.AbstractParamsEM

setUpdateMode(boolean, boolean, boolean) - Method in class EM_LLR_Utils.AbstractParamsEM

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

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

shuffleExpressions() - Method in class math_utils.ExpressionMatrix

similarities - Variable in class math_utils.SimilarityMatrix

SimilarityMatrix - Class in math_utils

SimilarityMatrix() - Constructor for class math_utils.SimilarityMatrix

SimilarityMatrix(String) - Constructor for class math_utils.SimilarityMatrix

SingletonsAndMetaModulesMerger - Class in graph_algorithms

SingletonsAndMetaModulesMerger(Collection<MetaModule>, ArrayList<Integer>, MetaModuleFinder) - Constructor for class graph_algorithms.SingletonsAndMetaModulesMerger

size() - Method in class math_utils.SimilarityMatrix

sortEdgesByScores(LinkedList<ComparableEdge>, Hashtable<Integer, HashSet<Integer>>) - Static method in class graph_algorithms.MetaModuleFinder

Static auxiliary methods

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

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

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

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

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

standardize() - Method in class math_utils.SimilarityMatrix

standardizeByClasses(int[]) - Method in class math_utils.ExpressionMatrix

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

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

staticMathHelperMethods - Class in math_utils

staticMathHelperMethods() - Constructor for class math_utils.staticMathHelperMethods