Uses of Class
ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Packages that use ExpressionExperimentManipulatingCLI

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.

Uses of ExpressionExperimentManipulatingCLI in ubic.gemma.apps

Subclasses of ExpressionExperimentManipulatingCLI in ubic.gemma.apps

Modifier and Type	Class	Description
class	AffyDataFromCelCli	Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
class	BatchEffectPopulationCli	For bulk processing of batch-info-fetching.
class	CellLevelMetadataWriterCli
class	DeleteDiffExCli	Delete differential expression analsyes on a per-experiment basis.
class	DeleteExperimentsCli	Delete one or more experiments from the system.
class	DetectQuantitationTypeCli
class	DifferentialExpressionAnalysisCli	A command line interface to the DifferentialExpressionAnalysis.
class	DifferentialExpressionAnalysisWriterCli	Writes differential expression analysis files to disk.
class	ExperimentalDesignImportCli
class	ExperimentalDesignWriterCLI	Writes out the experimental design for a given experiment.
class	ExpressionDataCorrMatCli	Create correlation visualizations for expression experiments
class	ExpressionDataMatrixWriterCLI	Prints preferred data matrix to a file.
class	ExpressionExperimentDataFileGeneratorCli	Deprecated. use DifferentialExpressionAnalysisWriterCli instead.
class	ExpressionExperimentDataUpdaterCli	Update GEO data for an experiment.
class	ExpressionExperimentMetadataChangelogEntryAdderCli	CLI tool for adding manual entries to the changelog file of an experiment.
class	ExpressionExperimentMetadataChangelogViewerCli	CLI tool for viewing the changelog file of an experiment.
class	ExpressionExperimentMetadataFileAdderCli	Add a metadata file to an experiment and record an entry in the changelog file.
class	ExpressionExperimentPlatformSwitchCli	Switch the array design used to the merged one.
class	ExpressionExperimentPrimaryPubCli	Update the primary publication for experiments.
class	ExpressionExperimentVectorsManipulatingCli<T extends DataVector>	Base class for CLI tools that manipulate expression experiment vectors.
class	GeeqCli	Generate or update GEEQ scores
class	LinkAnalysisCli	Commandline tool to conduct link (coexpression) analysis.
class	ListQuantitationTypesCli
class	LockExpressionDataFileCli	This CLI allows one to lock an experiment data or metadata file.
class	MakeExperimentPrivateCli
class	MakeExperimentsPublicCli	Make data sets public.
class	OrderVectorsByDesignCli	Use to change the order of the values to match the experimental design.
class	ProcessedDataComputeCLI	Prepare the "processed" expression data vectors, and can also do batch correction.
class	ProcessedDataDeleterCli
class	RawDataDeleterCli
class	RawExpressionDataWriterCli
class	RefreshExperimentCli
class	ReplaceDataCli	Replace data in an existing data set.
class	RNASeqBatchInfoCli	Deprecated. this should not be necessary and the regular batch population tool can be used instead.
class	RNASeqDataAddCli	Designed to add count and/or RPKM data to a data set that has only meta-data.
class	SingleCellDataAggregateDeleterCli
class	SingleCellDataAggregatorCli
class	SingleCellDataDeleterCli
class	SingleCellDataLoaderCli
class	SingleCellDataWriterCli
class	SingleCellSparsityMetricsUpdaterCli
class	SplitExperimentCli	Split an experiment into parts based on an experimental factor
class	SVDCli
class	VectorMergingCli	For experiments that used multiple array designs, merge the expression profiles