Uses of Package
ubic.gemma.model.expression.bioAssayData

Packages that use ubic.gemma.model.expression.bioAssayData

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.convert	Convert data from one QuantitationType to another.
ubic.gemma.core.analysis.preprocess.filter
ubic.gemma.core.analysis.preprocess.slice	This package provides capabilities for slicing BulkExpressionDataVector.
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This packge contains classes for splitting and aggregating single-cell data.
ubic.gemma.core.analysis.stats	This package contains classes for computing various statistics.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata	This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.core.visualization
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization
ubic.gemma.web.taglib

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.apps

Class	Description
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.cli.util

Class	Description
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.expression.coexpression.links

Class	Description
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.

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

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.preprocess

Class	Description
MeanVarianceRelation
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.preprocess.convert

Class	Description
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.preprocess.filter

Class	Description
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.preprocess.slice

Class	Description
BulkExpressionDataVector	A data vector storing bulk expression data.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.preprocess.svd

Class	Description
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.

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

Class	Description
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.singleCell

Class	Description
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.singleCell.aggregate

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.analysis.stats

Class	Description
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.datastructure.matrix

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BulkExpressionDataVector	A data vector storing bulk expression data.
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.datastructure.matrix.io

Class	Description
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.loader.expression.singleCell

Class	Description
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.loader.expression.singleCell.metadata

Class	Description
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.core.visualization

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BulkExpressionDataVector	A data vector storing bulk expression data.
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

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

Class	Description
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.model.analysis.expression.coexpression

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.model.analysis.expression.pca

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.model.common.quantitationtype

Class	Description
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.model.expression.bioAssayData

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BioAssayDimensionValueObject
BulkExpressionDataVector	A data vector storing bulk expression data.
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.
DataVectorValueObject	Base class for value objects of BulkExpressionDataVector.
DesignElementDataVector	Data vector associated to a CompositeSequence.
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.
ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
ExperimentExpressionLevelsValueObject.VectorElementValueObject
MeanVarianceRelation
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.
SlicedDoubleVectorValueObject

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.model.expression.experiment

Class	Description
MeanVarianceRelation
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

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

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.persistence.service.common.quantitationtype

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BulkExpressionDataVector	A data vector storing bulk expression data.
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.persistence.service.expression.bioAssay

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.persistence.service.expression.bioAssayData

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BioAssayDimensionValueObject
BulkExpressionDataVector	A data vector storing bulk expression data.
DesignElementDataVector	Data vector associated to a CompositeSequence.
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.
ExperimentExpressionLevelsValueObject
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.persistence.service.expression.experiment

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
BulkExpressionDataVector	A data vector storing bulk expression data.
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.
MeanVarianceRelation
ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.persistence.util

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
CellLevelCharacteristics	Characteristics applicable to individual cells in a SingleCellDimension.
CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
DesignElementDataVector	Data vector associated to a CompositeSequence.
SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.rest

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
CellLevelCharacteristicsValueObject
ExperimentExpressionLevelsValueObject
SingleCellDimensionValueObject	Value object for a single-cell dimension.

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

Class	Description
DesignElementDataVector	Data vector associated to a CompositeSequence.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.web.controller.expression.experiment

Class	Description
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.web.controller.visualization

Class	Description
DoubleVectorValueObject	Value object for a BulkExpressionDataVector containing doubles.

Classes in ubic.gemma.model.expression.bioAssayData used by ubic.gemma.web.taglib

Class	Description
BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.