Uses of Class
ubic.gemma.core.loader.expression.geo.model.GeoSeries

Packages that use GeoSeries

Package	Description
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.model
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.persistence.service.expression.experiment

Uses of GeoSeries in ubic.gemma.core.loader.expression.geo

Methods in ubic.gemma.core.loader.expression.geo that return types with arguments of type GeoSeries

Modifier and Type	Method	Description
Map<String,GeoSeries>	GeoParseResult.getSeries()
Map<String,GeoSeries>	GeoParseResult.getSeriesMap()

Methods in ubic.gemma.core.loader.expression.geo with parameters of type GeoSeries

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	GeoConverter.convert(GeoSeries geoSeries)
Collection<ExpressionExperiment>	GeoConverter.convert(GeoSeries geoSeries, boolean skipDataVectors)
Collection<ExpressionExperiment>	GeoConverterImpl.convert(GeoSeries geoSeries)
Collection<ExpressionExperiment>	GeoConverterImpl.convert(GeoSeries geoSeries, boolean skipDataVectors)
GeoSampleCorrespondence	DatasetCombiner.findGSECorrespondence(GeoSeries series)	Try to line up samples across datasets contained in a series.
static Map<GeoPlatform,List<GeoSample>>	DatasetCombiner.getPlatformSampleMap(GeoSeries geoSeries)
void	GeoDomainObjectGenerator.processDataSet(GeoSeries series, String dataSetAccession, GeoFamilyParser parser)	Process a data set and add it to the series

Uses of GeoSeries in ubic.gemma.core.loader.expression.geo.model

Methods in ubic.gemma.core.loader.expression.geo.model that return types with arguments of type GeoSeries

Modifier and Type	Method	Description
Collection<GeoSeries>	GeoDataset.getSeries()

Methods in ubic.gemma.core.loader.expression.geo.model with parameters of type GeoSeries

Modifier and Type	Method	Description
void	GeoDataset.addSeries(GeoSeries newSeries)
void	GeoDataset.dissociateFromSeries(GeoSeries s)	This is used when we break a series up into two, along organism lines.

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

Methods in ubic.gemma.core.loader.expression.geo.singleCell with parameters of type GeoSeries

Modifier and Type	Method	Description
Path	AbstractSingleFileInSeriesSingleCellDetector.downloadSingleCellData(GeoSeries series)	Download single-cell data for the given GEO series.
Path	AbstractSingleFileInSeriesSingleCellDetector.downloadSingleCellData(GeoSeries series, String file)	Download a specific supplementary file at the series-level.
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series)	Download single-cell data from a GEO series to disk.
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a sample in the context of a series.
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample, SingleCellDataType dataType)
void	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, SingleCellDataType dataType)
void	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, SingleCellDataType dataType, String supplementaryFile)
Path	MexDetector.downloadSingleCellData(GeoSeries series)
Path	MexDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a GEO sample within the context of its series.
Path	SeriesAwareSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)
Path	SingleCellDetector.downloadSingleCellData(GeoSeries series)	Download single-cell data for the given GEO series.
List<String>	AbstractSingleFileInSeriesSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries sample)
List<String>	GeoSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series)
List<String>	GeoSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	MexDetector.getAdditionalSupplementaryFiles(GeoSeries series)
List<String>	MexDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	SeriesAwareSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	SingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series)	Obtain a list of all additional supplementary files.
Set<SingleCellDataType>	GeoSingleCellDetector.getAllSingleCellDataTypes(GeoSeries series)	Obtain all single-cell data types a GEO series contains.
protected Path	AbstractSingleFileInSeriesSingleCellDetector.getDest(GeoSeries series)	Obtain the download destination for the single-cell data file.
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.
SingleCellDataType	GeoSingleCellDetector.getSingleCellDataType(GeoSeries series)	Determine the type of single-cell data a GEO series contains.
boolean	AbstractSingleFileInSeriesSingleCellDetector.hasSingleCellData(GeoSeries series)
boolean	GeoSingleCellDetector.hasSingleCellData(GeoSeries series)	Detects if a GEO series has single-cell data either at the series-level or in individual samples.
boolean	GeoSingleCellDetector.hasSingleCellData(GeoSeries series, GeoSample sample)
boolean	MexDetector.hasSingleCellData(GeoSeries series)	Indicate if the given GEO series has single-cell data.
boolean	MexDetector.hasSingleCellData(GeoSeries series, GeoSample sample)	Check if a sample contains single-cell data in the context of its series.
boolean	SeriesAwareSingleCellDetector.hasSingleCellData(GeoSeries series, GeoSample sample)
boolean	SingleCellDetector.hasSingleCellData(GeoSeries series)	Indicate if the given GEO series has single-cell data.
boolean	GeoSingleCellDetector.hasSingleCellDataInSeries(GeoSeries series)	Check if a GEO series has single-cell data at the series-level.
boolean	GeoSingleCellDetector.hasSingleCellDataInSeries(GeoSeries series, SingleCellDataType dataType)	Check if a GEO series has single-cell data at the series-level.
boolean	GeoSingleCellDetector.hasSingleCellDataInSra(GeoSeries series)	Check if a GEO series has single-cell data in SRA.
boolean	GeoSingleCellDetector.hasSingleCellDataInSra(GeoSeries series, Collection<String> sraAccessions, Collection<String> sraAccessionsWithOtherDataTypes)

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

Modifier	Constructor	Description
	GeoMexSingleCellDataLoaderConfigurer(Path mexDir, GeoSeries series, Path cellRangerPrefix)

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

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

Modifier	Constructor	Description
	MexSingleCellDataLoaderConfigurer(Path mexDir, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper, Path cellRangerPrefix, GeoSeries geoSeries)

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

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

Modifier and Type	Method	Description
GeoSeries	ExpressionExperimentGeoService.getGeoSeries(ExpressionExperiment ee)	Obtain the GEO series metadata.
GeoSeries	ExpressionExperimentGeoServiceImpl.getGeoSeries(ExpressionExperiment ee)