Uses of Interface
ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader

Packages that use SingleCellDataLoader

Package	Description
ubic.gemma.core.loader.expression.cellxgene	This package contains classes for loading expression data from CELLxGENE.
ubic.gemma.core.loader.expression.geo.singleCell	This package contains specific logic for dealing with single-cell data from GEO.
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.

Uses of SingleCellDataLoader in ubic.gemma.core.loader.expression.cellxgene

Classes in ubic.gemma.core.loader.expression.cellxgene that implement SingleCellDataLoader

Modifier and Type	Class	Description
class	CellXGeneAnnDataSingleCellDataLoader

Methods in ubic.gemma.core.loader.expression.cellxgene with parameters of type SingleCellDataLoader

Modifier and Type	Method	Description
ExpressionExperiment	CellXGeneConverter.convert(CollectionMetadata collectionMetadata, DatasetMetadata datasetMetadata, ArrayDesign platform, Collection<CompositeSequence> compositeSequences, String datasetShortName, SingleCellDataLoader dataLoader, boolean loadSingleCellData)

Uses of SingleCellDataLoader in ubic.gemma.core.loader.expression.geo.singleCell

Methods in ubic.gemma.core.loader.expression.geo.singleCell that return SingleCellDataLoader

Modifier and Type	Method	Description
SingleCellDataLoader	AnnDataDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)
SingleCellDataLoader	GeoSingleCellDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single-cell data loader.
SingleCellDataLoader	LoomSingleCellDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)
SingleCellDataLoader	MexDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)
SingleCellDataLoader	SeuratDiskDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)
SingleCellDataLoader	SingleCellDetector.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single cell data loader for the given GEO series based on previously downloading data.

Uses of SingleCellDataLoader in ubic.gemma.core.loader.expression.singleCell

Classes in ubic.gemma.core.loader.expression.singleCell with type parameters of type SingleCellDataLoader

Modifier and Type	Interface	Description
interface	SingleCellDataLoaderConfigurer<T extends SingleCellDataLoader>	Interface for configuring a single-cell data loader.

Classes in ubic.gemma.core.loader.expression.singleCell that implement SingleCellDataLoader

Modifier and Type	Class	Description
class	AbstractDelegatingSingleCellDataLoader
class	AnnDataSingleCellDataLoader	Reads single-cell vectors from the AnnData on-disk HDF5 format.
class	MexSingleCellDataLoader	Load single cell data from 10X Genomics MEX format.
class	NullSingleCellDataLoader	Single-cell data loader used when no data is available.
class	SequencingMetadataFileSingleCellDataLoader	Adapt a SequencingMetadataFileDataLoader so that it can be used as a SingleCellDataLoader.

Constructors in ubic.gemma.core.loader.expression.singleCell with parameters of type SingleCellDataLoader

Modifier	Constructor	Description
protected	AbstractDelegatingSingleCellDataLoader(SingleCellDataLoader delegate)
	SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)

Uses of SingleCellDataLoader in ubic.gemma.core.loader.expression.singleCell.metadata

Classes in ubic.gemma.core.loader.expression.singleCell.metadata that implement SingleCellDataLoader

Modifier and Type	Class	Description
class	GenericMetadataSingleCellDataLoader	A generic loader that can be used to load single-cell data with a tabular metadata file.

Constructors in ubic.gemma.core.loader.expression.singleCell.metadata with parameters of type SingleCellDataLoader

Modifier	Constructor	Description
	GenericMetadataSingleCellDataLoader(SingleCellDataLoader delegate, Path cellTypeMetadataFile, Path otherCellCharacteristicsMetadataFile, List<String> otherCellLevelCharacteristicsNames, List<String> otherCellLevelCharacteristicsDefaultValues, List<String> otherCellLevelCharacteristicsDefaultValueUris)