Uses of Package
ubic.gemma.model.expression.experiment
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.expression Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.expression.coexpression.links Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.expression.diff Class Description BioAssaySet Represents a set of BioAssays.ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExperimentalFactorValueObject ExpressionExperiment ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentExpressionExperimentValueObject FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Statement A special kind of characteristic that act as a statement. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.batcheffects Class Description BatchEffectType Represents a batch effect.BioAssaySet Represents a set of BioAssays.ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment ExpressionExperimentSubSet A subset of samples from an ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.filter Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.svd Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.report Class Description ExpressionExperiment ExpressionExperimentDetailsValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.service Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.apps Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.datastructure.matrix Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant" -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.entrez.pubmed Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.arrayDesign Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.geo Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.simple Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.ontology Class Description FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"StatementValueObject Represents a VO for aStatement, typically part of aFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.search Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.search.source Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.coexp Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.diffex Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.expression Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.maintenance Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.visualization Class Description ExpressionExperimentDetailsValueObject ExpressionExperimentValueObject FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.visualization Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis Class Description BioAssaySet Represents a set of BioAssays. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis.expression Class Description BioAssaySet Represents a set of BioAssays.ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration). -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis.expression.coexpression Class Description BioAssaySet Represents a set of BioAssays. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis.expression.diff Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExperimentalFactorValueObject ExpressionExperimentValueObject FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"FactorValueBasicValueObject Each factorvalue can be associated with multiple characteristics (or with a measurement).FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.association.coexpression Class Description BioAssaySet Represents a set of BioAssays. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.description Class Description ExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.quantitationtype Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.bioAssayData Class Description ExpressionExperiment ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.biomaterial Class Description FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant" -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.experiment Class Description AbstractFactorValueValueObject The bare minimum to represent a factor value.BatchEffectType Represents a batch effect.BioAssaySet Represents a set of BioAssays.ExperimentalDesign ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExperimentalFactorValueObject ExpressionExperiment ExpressionExperimentSetValueObject ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentExpressionExperimentValueObject FactorType FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Geeq Represents quality information about a data set.GeeqValueObject Represents publicly available geeq informationSessionBoundExpressionExperimentSetValueObject Statement A special kind of characteristic that act as a statement.StatementValueObject Represents a VO for aStatement, typically part of aFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.persister Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis Class Description BioAssaySet Represents a set of BioAssays. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment ExpressionExperimentDetailsValueObject ExpressionExperimentSetValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression.coexpression Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression.diff Class Description BioAssaySet Represents a set of BioAssays.ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment ExpressionExperimentDetailsValueObject ExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression.pca Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression.sampleCoexpression Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.association.coexpression Class Description BioAssaySet Represents a set of BioAssays. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.blacklist Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.common.description Class Description ExpressionExperiment Statement A special kind of characteristic that act as a statement. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.common.quantitationtype Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.arrayDesign Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.bioAssayData Class Description BioAssaySet Represents a set of BioAssays.ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.biomaterial Class Description ExpressionExperiment -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.experiment Class Description BioAssaySet Represents a set of BioAssays.ExperimentalDesign ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExperimentalFactorValueObject ExpressionExperiment ExpressionExperimentDetailsValueObject ExpressionExperimentSetValueObject ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentExpressionExperimentValueObject FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject.Geeq Represents quality information about a data set.GeeqValueObject Represents publicly available geeq informationStatement A special kind of characteristic that act as a statement. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.util Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperiment ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentFactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant" -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest Class Description BatchEffectType Represents a batch effect.ExpressionExperiment ExpressionExperimentSubSet A subset of samples from an ExpressionExperimentExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest.serializers Class Description AbstractFactorValueValueObject The bare minimum to represent a factor value.FactorValueBasicValueObject Each factorvalue can be associated with multiple characteristics (or with a measurement).FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest.util.args Class Description ExpressionExperiment ExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.diff Class Description ExperimentalFactorValueObject ExpressionExperimentSetValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.expression.biomaterial Class Description FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.expression.experiment Class Description ExperimentalDesign ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExperimentalFactorValueObject ExpressionExperiment ExpressionExperimentDetailsValueObject ExpressionExperimentSetValueObject ExpressionExperimentValueObject FactorValue The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"FactorValueValueObject Deprecated.aim towards using theFactorValueBasicValueObject.SessionBoundExpressionExperimentSetValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.visualization Class Description ExperimentalFactor ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).ExpressionExperimentDetailsValueObject ExpressionExperimentValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.persistence Class Description ExpressionExperimentDetailsValueObject SessionBoundExpressionExperimentSetValueObject -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.util Class Description ExperimentalDesign ExpressionExperiment