Package ubic.gemma.model.expression.experiment

package ubic.gemma.model.expression.experiment

Class	Description
AbstractFactorValueValueObject	The bare minimum to represent a factor value.
AgentCurationKind	Discriminator on AgentProposal rows: 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).
BatchEffectType	Represents a batch effect.
BioAssaySet	Represents a set of BioAssays.
BioAssaySetValueObject	Interface for VOs deriving from BioAssaySet.
DesignApplyOutcome	Outcome returned by the PUT /datasets/{id}/design apply path.
DesignPreflightReport	Report returned by POST /datasets/{id}/designPreflight.
DesignPreflightReport.AnalysisRef
DesignPreflightReport.Blocker	One reason the proposed payload cannot be applied.
DesignPreflightReport.EntityRef
DesignPreflightReport.SubsetRef
DesignPreflightReport.Summary
ExperimentalDesign	Hibernate Search 7 mapping: indexed root and embedded contributor to ExpressionExperiment.getExperimentalDesign().
ExperimentalDesign.Factory
ExperimentalDesignUtils
ExperimentalDesignValueObject	Full structural representation of an ExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.
ExperimentalDesignValueObject.BioMaterialFactorValueAssignment	Assignment of a single BioMaterial (sample) to its assigned FactorValues.
ExperimentalDesignValueObject.ExperimentalFactorEntry	One ExperimentalFactor, with its factor values inlined.
ExperimentalFactor	ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
ExperimentalFactor.Factory
ExperimentalFactorValueObject
ExperimentFactorUtils
ExpressionExperiment	Hibernate Search 7 indexed root.
ExpressionExperiment.Factory
ExpressionExperimentDetailsValueObject
ExpressionExperimentIdAndShortName	A minimalistic projection of an ExpressionExperiment.
ExpressionExperimentReferenceValueObject	Compact dataset identity — enough to name a dataset and link to it.
ExpressionExperimentSetValueObject
ExpressionExperimentSubSet	A subset of assays (or derived assays) from an ExpressionExperiment.
ExpressionExperimentSubSet.Factory
ExpressionExperimentSubSetUtils	Utility methods for ExpressionExperimentSubSet.
ExpressionExperimentSubsetValueObject
ExpressionExperimentValueObject
FactorType
FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
FactorValue.Factory
FactorValueBasicValueObject	Each factorvalue can be associated with multiple characteristics (or with a measurement).
FactorValueUtils
FactorValueValueObject	Deprecated. aim towards using the FactorValueBasicValueObject.
FreeTextExpressionExperimentResultsValueObject
Geeq	Represents quality information about a data set.
GeeqAdminValueObject	Represents administrative geeq information.
GeeqValueObject	Represents publicly available geeq information
GeoScrapeWatermark	Append-only record of one GEO scrape run.
GeoScrapeWatermark.Status	Lifecycle status of a scrape run.
PreboardedExperiment	Subclass of Investigation representing a proposed-but-not-yet-loaded dataset.
SessionBoundExpressionExperimentSetValueObject
Statement	A special kind of characteristic that act as a statement.
Statement.Factory
StatementUtils
StatementValueObject	Represents a VO for a Statement, typically part of a FactorValueBasicValueObject.
WorkflowState	Eight-state workflow lifecycle for experiments (and forthcoming PreboardedExperiments).