Uses of Package
ubic.gemma.model.expression.experiment
Packages that use ubic.gemma.model.expression.experiment
Package
Description
This package contains built-in Gemma CLI applications.
This package contains classes for preprocessing expression data.
This package contains classes for analysing single-cell expression data.
This package contains classes for subsetting and aggregating single-cell data.
This package contains data structures for representing matrices of gene expression.
This package contains I/O utilities for reading and writing expression data matrices.
This package contains interfaces and classes for loading expression data.
This package contains classes for loading expression data from CELLxGENE.
This package contains classes for loading single-cell expression data.
Utilities for mapping
Identifiable entities to external identifiers.This package contains classes related to the Cell Browser visualization tool.
Service for managing blacklisted entities.
Contains classes related to database maintenance.
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.apps
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.cli.utilClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.expression
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.expression.diffClassDescriptionRepresents a set of
BioAssays.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from anExpressionExperiment.The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"A special kind of characteristic that act as a statement. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocessClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.batcheffectsClassDescriptionRepresents a batch effect.Represents a set of
BioAssays.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from anExpressionExperiment. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.svdClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.report
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.service
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.singleCellClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from an
ExpressionExperiment.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.analysis.singleCell.aggregateClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from an
ExpressionExperiment.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.datastructure.matrixClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.datastructure.matrix.ioClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.entrez.pubmed
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expressionClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.geo
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.simple
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.expression.singleCellClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.loader.util.mapper
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.ontologyClassDescriptionThe value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Represents a VO for a
Statement, typically part of aFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.search
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.search.source
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.coexp
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.diffexClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.analysis.expression
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.maintenance
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.tasks.visualizationClassDescriptionDeprecated.
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.visualizationClassDescriptionRepresents a set of
BioAssays.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from anExpressionExperiment. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.visualization.cellbrowserClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis.expressionClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.analysis.expression.diffClassDescriptionRepresents a set of
BioAssays.Interface for VOs deriving fromBioAssaySet.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Each factorvalue can be associated with multiple characteristics (or with a measurement).Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.association.coexpression
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.description
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.quantitationtype
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.search
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.bioAssay
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.bioAssayData
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.biomaterialClassDescriptionThe value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Each factorvalue can be associated with multiple characteristics (or with a measurement).Deprecated.aim towards using the
FactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.experimentClassDescriptionThe bare minimum to represent a factor value.Represents a batch effect.Represents a set of
BioAssays.Interface for VOs deriving fromBioAssaySet.One reason the proposed payload cannot be applied.Assignment of a singleBioMaterial(sample) to its assignedFactorValues.OneExperimentalFactor, with its factor values inlined.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A minimalistic projection of anExpressionExperiment.A subset of assays (or derived assays) from anExpressionExperiment.The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Each factorvalue can be associated with multiple characteristics (or with a measurement).Deprecated.aim towards using theFactorValueBasicValueObject.Represents quality information about a data set.Represents publicly available geeq informationSubclass ofInvestigationrepresenting a proposed-but-not-yet-loaded dataset.A special kind of characteristic that act as a statement.Represents a VO for aStatement, typically part of aFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.persister
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.analysis.expression.diffClassDescriptionRepresents a set of
BioAssays.Interface for VOs deriving fromBioAssaySet.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration). -
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.blacklist
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.common.descriptionClassDescriptionA minimalistic projection of an
ExpressionExperiment.A special kind of characteristic that act as a statement. -
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.biomaterialClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.experimentClassDescriptionReport returned by
POST /datasets/{id}/designPreflight.Full structural representation of anExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from anExpressionExperiment.The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Deprecated.aim towards using theFactorValueBasicValueObject.Represents quality information about a data set.Represents publicly available geeq informationA special kind of characteristic that act as a statement. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.maintenance
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.utilClassDescriptionRepresents a set of
BioAssays.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).A subset of assays (or derived assays) from anExpressionExperiment.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.restClassDescriptionRepresents a batch effect.Interface for VOs deriving from
BioAssaySet.Report returned byPOST /datasets/{id}/designPreflight.Full structural representation of anExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.A subset of assays (or derived assays) from anExpressionExperiment.The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Each factorvalue can be associated with multiple characteristics (or with a measurement).Represents publicly available geeq information -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest.serializersClassDescriptionThe bare minimum to represent a factor value.Each factorvalue can be associated with multiple characteristics (or with a measurement).Deprecated.aim towards using the
FactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest.util.argsClassDescriptionReport returned by
POST /datasets/{id}/designPreflight.Full structural representation of anExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.A subset of assays (or derived assays) from anExpressionExperiment. -
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.expression.biomaterialClassDescriptionThe value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Deprecated.aim towards using the
FactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.expression.experimentClassDescriptionInterface for VOs deriving from
BioAssaySet.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"Each factorvalue can be associated with multiple characteristics (or with a measurement).Deprecated.aim towards using theFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.persistence
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.web.controller.visualizationClassDescriptionInterface for VOs deriving from
BioAssaySet.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.web.service
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FactorValueBasicValueObject.