Uses of Package
ubic.gemma.model.analysis.expression.diff

Packages that use ubic.gemma.model.analysis.expression.diff

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.service
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.tasks.visualization
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.cli.util

Class	Description
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.core.analysis.expression.diff

Class	Description
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
DifferentialExpressionValueObject	Represents the results for one probe.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.
GeneDifferentialExpressionMetaAnalysisDetailValueObject
GeneDifferentialExpressionMetaAnalysisSummaryValueObject

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.core.analysis.service

Class	Description
Baseline	Represents a baseline for a single factor or an interaction of factors.
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.core.tasks.analysis.diffex

Class	Description
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.core.tasks.visualization

Class	Description
DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis
DiffExResultSetSummaryValueObject	Summary of a result set.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.model.analysis.expression.diff

Class	Description
Baseline	Represents a baseline for a single factor or an interaction of factors.
Contrast	Represents a contrast.
ContrastResult	Represents a contrast between "conditions".
ContrastResultValueObject	Represents a contrast result.
ContrastsValueObject	Stores selected details of the contrasts for a single DifferentialExpressionResult
ContrastVO	Helper object, not for general use.
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
DifferentialExpressionAnalysisResultValueObject	Unlike DiffExResultSetSummaryValueObject, this value object is meant for the public API.
DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis
DiffExResultSetSummaryValueObject	Summary of a result set.
DiffExResultSetSummaryValueObject.Prefetch	Pre-aggregated experimentalFactors + baselineGroup for a single ExpressionAnalysisResultSet, sourced from a batched join-fetch query so the VO ctor avoids three sequential lazy initializations.
Direction	Represents the direction of a change e.g.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.
GeneDifferentialExpressionMetaAnalysisResult
GeneDifferentialExpressionMetaAnalysisResultValueObject
HitListSize	The number of probes meeting a given q-value threshold in the result set.
IncludedResultSetInfoValueObject
PvalueDistribution
ResultSetCountsValueObject	Cacheable, immutable snapshot of the per-result-set hit-list counts displayed by DiffExResultSetSummaryValueObject.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.model.expression.experiment

Class	Description
DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.persistence.service.analysis.expression.diff

Class	Description
Baseline	Represents a baseline for a single factor or an interaction of factors.
ContrastsValueObject	Stores selected details of the contrasts for a single DifferentialExpressionResult
DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
DifferentialExpressionAnalysisResultSetValueObject	Wraps an ExpressionAnalysisResultSet and expose it to the public API.
DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis
DifferentialExpressionValueObject	Represents the results for one probe.
DiffExprGeneSearchResult	Value object for differential expression result for one result - corresponds to the DifferentialExpressionAnalysisResults for one gene in one ResultSet (combined for multiple probes), but represents only the "selected" analysisResult.
DiffExResultSetSummaryValueObject	Summary of a result set.
DiffExResultSetSummaryValueObject.Prefetch	Pre-aggregated experimentalFactors + baselineGroup for a single ExpressionAnalysisResultSet, sourced from a batched join-fetch query so the VO ctor avoids three sequential lazy initializations.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.
GeneDifferentialExpressionMetaAnalysisResult
GeneDifferentialExpressionMetaAnalysisResultValueObject
GeneDifferentialExpressionMetaAnalysisSummaryValueObject
IncludedResultSetInfoValueObject
ResultSetCountsValueObject	Cacheable, immutable snapshot of the per-result-set hit-list counts displayed by DiffExResultSetSummaryValueObject.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.persistence.util

Class	Description
DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.rest

Class	Description
Baseline	Represents a baseline for a single factor or an interaction of factors.
DifferentialExpressionAnalysisResult	Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor.
DifferentialExpressionAnalysisResultSetValueObject	Wraps an ExpressionAnalysisResultSet and expose it to the public API.
DifferentialExpressionAnalysisResultValueObject	Unlike DiffExResultSetSummaryValueObject, this value object is meant for the public API.
DifferentialExpressionAnalysisValueObject	Summary of a differential expression analysis
DifferentialExpressionValueObject	Represents the results for one probe.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.

Classes in ubic.gemma.model.analysis.expression.diff used by ubic.gemma.rest.util.args

Class	Description
DifferentialExpressionAnalysisResultSetValueObject	Wraps an ExpressionAnalysisResultSet and expose it to the public API.
ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.