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.audit
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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).Hibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root.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).Hibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root.A subset of assays (or derived assays) from anExpressionExperiment. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.preprocess.qc
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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).Hibernate Search 7 indexed root.
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.analysis.reportClassDescriptionHibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root.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).Hibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root.
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.core.geoscrape
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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).Hibernate Search 7 indexed root.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).Hibernate Search 7 indexed root.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.diffexClassDescriptionExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).Hibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root.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).Hibernate Search 7 indexed root.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.analysisClassDescriptionRepresents a set of
BioAssays.Hibernate Search 7 indexed root.Eight-state workflow lifecycle for experiments (and forthcomingPreboardedExperiments). -
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).Hibernate Search 7 indexed root.
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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.Hibernate Search 7 mapping: indexed root and embedded contributor toExpressionExperiment.getExperimentalDesign().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.analysis.expression.pca
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.auditAndSecurity.curationClassDescriptionDiscriminator on
AgentProposalrows: which kind of agent activity a row records — a forward-looking proposal (pre-curation suggestion), an audit (a post-hoc review of an existing dataset, reporting findings to act on), or an evaluation (a scored assessment of curation that already exists). -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.common.descriptionClassDescriptionHibernate Search 7 indexed root.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.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.biomaterialClassDescriptionHibernate Search 7 indexed root.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 the
FactorValueBasicValueObject.Represents a VO for aStatement, typically part of aFactorValueBasicValueObject. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.expression.experimentClassDescriptionThe bare minimum to represent a factor value.Discriminator on
AgentProposalrows: which kind of agent activity a row records — a forward-looking proposal (pre-curation suggestion), an audit (a post-hoc review of an existing dataset, reporting findings to act on), or an evaluation (a scored assessment of curation that already exists).Represents a batch effect.Represents a set ofBioAssays.Interface for VOs deriving fromBioAssaySet.Report returned byPOST /datasets/{id}/designPreflight.One reason the proposed payload cannot be applied.Hibernate Search 7 mapping: indexed root and embedded contributor toExpressionExperiment.getExperimentalDesign().Full structural representation of anExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.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).Hibernate Search 7 indexed root.A minimalistic projection of anExpressionExperiment.Compact dataset identity — enough to name a dataset and link to it.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 informationLifecycle status of a scrape run.A special kind of characteristic that act as a statement.Represents a VO for aStatement, typically part of aFactorValueBasicValueObject.Eight-state workflow lifecycle for experiments (and forthcomingPreboardedExperiments). -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.model.pipeline
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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.expressionClassDescriptionHibernate Search 7 indexed root.
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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).Hibernate Search 7 indexed root. -
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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.auditAndSecurity.curationClassDescriptionDiscriminator on
AgentProposalrows: which kind of agent activity a row records — a forward-looking proposal (pre-curation suggestion), an audit (a post-hoc review of an existing dataset, reporting findings to act on), or an evaluation (a scored assessment of curation that already exists). -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.common.descriptionClassDescriptionHibernate Search 7 indexed root.A 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.bioAssayClassDescriptionRepresents a set of
BioAssays.Hibernate Search 7 indexed root.A subset of assays (or derived assays) from anExpressionExperiment. -
Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.bioAssayData
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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).Hibernate Search 7 indexed root.
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.service.expression.experimentClassDescriptionOutcome returned by the
PUT /datasets/{id}/designapply path.Report returned byPOST /datasets/{id}/designPreflight.Hibernate Search 7 mapping: indexed root and embedded contributor toExpressionExperiment.getExperimentalDesign().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).Hibernate Search 7 indexed root.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 informationSubclass ofInvestigationrepresenting a proposed-but-not-yet-loaded dataset.A special kind of characteristic that act as a statement.Eight-state workflow lifecycle for experiments (and forthcomingPreboardedExperiments). -
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.service.pipeline
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.persistence.utilClassDescriptionRepresents a set of
BioAssays.Hibernate Search 7 mapping: indexed root and embedded contributor toExpressionExperiment.getExperimentalDesign().ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).Hibernate Search 7 indexed root.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.Hibernate Search 7 indexed root.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
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Classes in ubic.gemma.model.expression.experiment used by ubic.gemma.rest.util.argsClassDescriptionRepresents a set of
BioAssays.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.Hibernate Search 7 indexed root.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"
FactorValueBasicValueObject.