Uses of Class
ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

Packages that use ExpressionExperimentManipulatingCLI

Package	Description
ubic.gemma.core.apps

Uses of ExpressionExperimentManipulatingCLI in ubic.gemma.core.apps

Subclasses of ExpressionExperimentManipulatingCLI in ubic.gemma.core.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	DeleteDiffExCli	Delete differential expression analsyes on a per-experiment basis.
class	DeleteExperimentsCli	Delete one or more experiments from the system.
class	DifferentialExpressionAnalysisCli	A command line interface to the DifferentialExpressionAnalysis.
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
class	ExpressionExperimentPlatformSwitchCli	Switch the array design used to the merged one.
class	ExpressionExperimentPrimaryPubCli	Update the primary publication for experiments.
class	GeeqCli	Generate or update GEEQ scores
class	LinkAnalysisCli	Commandline tool to conduct link (coexpression) analysis.
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	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	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