Uses of Interface
ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix

Packages that use SingleCellExpressionDataMatrix

Package	Description
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
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.ucsc.cellbrowser	This package contains utilities for loading and interacting with the UCSC Cell Browser.
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.persistence.service.expression.experiment

Uses of SingleCellExpressionDataMatrix in ubic.gemma.core.analysis.singleCell.aggregate

Methods in ubic.gemma.core.analysis.singleCell.aggregate with parameters of type SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
static <T> BulkExpressionDataMatrix<T>	SingleCellDataVectorAggregatorUtils.aggregate(SingleCellExpressionDataMatrix<T> scMatrix, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, Class<T> scalarType)	Aggregate a single-cell data matrix.

Uses of SingleCellExpressionDataMatrix in ubic.gemma.core.datastructure.matrix

Classes in ubic.gemma.core.datastructure.matrix that implement SingleCellExpressionDataMatrix

Modifier and Type	Class	Description
class	AbstractSingleCellExpressionDataMatrix<T>
class	EmptySingleCellExpressionDataMatrix
class	SingleCellExpressionDataDoubleMatrix
class	SingleCellExpressionDataIntMatrix

Methods in ubic.gemma.core.datastructure.matrix that return SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
static SingleCellExpressionDataMatrix<?>	SingleCellExpressionDataMatrix.getMatrix(List<SingleCellExpressionDataVector> vectors)

Methods in ubic.gemma.core.datastructure.matrix with parameters of type SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
static List<SingleCellExpressionDataVector>	SingleCellExpressionDataMatrixUtils.toVectors(SingleCellExpressionDataMatrix<?> matrix)

Uses of SingleCellExpressionDataMatrix in ubic.gemma.core.datastructure.matrix.io

Methods in ubic.gemma.core.datastructure.matrix.io with parameters of type SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, OutputStream stream)
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, Writer stream)
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, OutputStream stream)	Write a MEX matrix as a TAR archive to the given output stream.
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Write a matrix to a directory.
default int	SingleCellExpressionDataMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, OutputStream stream)
default int	SingleCellExpressionDataMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Writer writer)
int	TabularMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, Writer writer)
int	TabularMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)

Uses of SingleCellExpressionDataMatrix in ubic.gemma.core.loader.expression.ucsc.cellbrowser

Methods in ubic.gemma.core.loader.expression.ucsc.cellbrowser that return SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
static SingleCellExpressionDataMatrix<?>	UcscCellBrowserUtils.getDatasetDataMatrix(String datasetId, QuantitationType quantitationType, Map<String,CompositeSequence> designElementsMap, Map<String,BioAssay> cellIdToAssayMap, ProgressReporter progressReporter)	Create a stream over the expression data matrix of a given dataset.

Uses of SingleCellExpressionDataMatrix in ubic.gemma.core.visualization.cellbrowser

Methods in ubic.gemma.core.visualization.cellbrowser with parameters of type SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
int	CellBrowserTabularMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, Writer writer)

Uses of SingleCellExpressionDataMatrix in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return SingleCellExpressionDataMatrix

Modifier and Type	Method	Description
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentService.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentService.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)