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.

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)