Uses of Class
ubic.gemma.cli.util.AbstractAutoSeekingCLI

Packages that use AbstractAutoSeekingCLI

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

Uses of AbstractAutoSeekingCLI in ubic.gemma.apps

Subclasses of AbstractAutoSeekingCLI 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	AffyProbeCollapseCli	Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
class	ArrayDesignAnnotationFileCli	Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
class	ArrayDesignAuditTrailCleanupCli	work in progress
class	ArrayDesignBioSequenceDetachCli	Remove all associations that this array design has with BioSequences.
class	ArrayDesignBlatCli	Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
class	ArrayDesignMapSummaryCli	CLI for ArrayDesignMapSummaryService
class	ArrayDesignMergeCli	make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
class	ArrayDesignProbeCleanupCLI	Delete design elements (probes) that are invalid for one reason or another.
class	ArrayDesignProbeMapperCli	Process the blat results for an array design to map them onto genes.
class	ArrayDesignProbeRenamerCli	Deprecated. renaming probes is not a good idea in general
class	ArrayDesignRepeatScanCli	Runs repeatmasker on array designs.
class	ArrayDesignSequenceAssociationCli	Attach sequences to array design, fetching from BLAST database if requested.
class	ArrayDesignSequenceManipulatingCli	Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
class	ArrayDesignSubsumptionTesterCli	Test two array designs to see if one subsumes the other, and if so update their information.
class	BatchEffectPopulationCli	For bulk processing of batch-info-fetching.
class	BioSequenceCleanupCli	Goes through the biosequences for array designs in the database and removes duplicates.
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	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
class	ExpressionExperimentDataUpdaterCli	Update GEO data for an experiment.
class	ExpressionExperimentManipulatingCLI	Base class for CLIs that needs one or more expression experiment as an input.
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