Uses of Package
ubic.gemma.core.datastructure.matrix
Packages that use ubic.gemma.core.datastructure.matrix
Package
Description
This package contains classes for preprocessing expression data.
Convert data from one
QuantitationType to another.This package contains classes for detecting and linting expression data.
This package contains classes for filtering 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 utilities for loading and interacting with the UCSC Cell Browser.
This package contains classes related to the Cell Browser visualization tool.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.expression.coexpression.linksClassDescriptionA data structure that holds a reference to the data for a given expression experiment.Encapsulates information about the row 'label' for a ExpressionDataMatrix.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.expression.diffClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocessClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocess.batcheffectsClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocess.convertClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocess.detectClassDescriptionA data structure that holds a reference to the data for a given expression experiment.Represents a matrix of data from an
ExpressionExperiment. -
Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocess.filterClassDescriptionMatrix of booleans mapped from an ExpressionExperiment.A data structure that holds a reference to the data for a given expression experiment.Represents a matrix of data from an
ExpressionExperiment. -
Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.preprocess.svdClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.serviceClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.analysis.singleCell.aggregateClassDescriptionInterface for bulk expression data matrices.In a single-cell expression data matrix, each column represents a cell.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.datastructure.matrixClassDescriptionBase class for bulk expression data matrices.Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.Interface for bulk expression data matrices.Interface for bulk expression data matrices that can be efficiently accessed as a primitive double matrix.Interface for bulk expression data matrices that can be efficiently accessed as a primitive int matrix.An empty bulk expression data matrix.Used to make a 'dummy matrix' that has the column information populated.Matrix of booleans mapped from an ExpressionExperiment.A data structure that holds a reference to the data for a given expression experiment.Warning, not fully tested.Represents a matrix of data from an
ExpressionExperiment.Encapsulates information about the row 'label' for a ExpressionDataMatrix.Interface for matrices that can provide unboxed doubles.A wrapper for anExpressionDataMatrixthat applies a mask to the data, allowing selective access to the underlying matrix.An interface for bulk matrices that supports multipleBioAssayperBioMaterial.ABulkExpressionDataMatrixthat was derived from aSingleCellExpressionDataMatrix.In a single-cell expression data matrix, each column represents a cell. -
Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.datastructure.matrix.ioClassDescriptionInterface for bulk expression data matrices.Represents a matrix of data from an
ExpressionExperiment.In a single-cell expression data matrix, each column represents a cell. -
Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.loader.expressionClassDescriptionA data structure that holds a reference to the data for a given expression experiment.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.loader.expression.ucsc.cellbrowserClassDescriptionIn a single-cell expression data matrix, each column represents a cell.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.core.visualization.cellbrowserClassDescriptionIn a single-cell expression data matrix, each column represents a cell.
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Classes in ubic.gemma.core.datastructure.matrix used by ubic.gemma.persistence.service.expression.experimentClassDescriptionIn a single-cell expression data matrix, each column represents a cell.