@ParametersAreNonnullByDefault

Package ubic.gemma.apps

This package contains built-in Gemma CLI applications.

For third-party applications, use ubic.gemma.contrib.apps instead.

Class Summary

Class	Description
AffyDataFromCelCli	Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
AffyProbeCollapseCli	Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
ArrayDesignAlternativePopulateCli	This only needs to be re-run when the mappings change.
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.
ArrayDesignAuditTrailCleanupCli	work in progress
ArrayDesignBioSequenceDetachCli	Remove all associations that this array design has with BioSequences.
ArrayDesignBlatCli	Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
ArrayDesignMapSummaryCli	CLI for ArrayDesignMapSummaryService
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.
ArrayDesignProbeCleanupCLI	Delete design elements (probes) that are invalid for one reason or another.
ArrayDesignProbeMapperCli	Process the blat results for an array design to map them onto genes.
ArrayDesignProbeRenamerCli	Deprecated. renaming probes is not a good idea in general
ArrayDesignRepeatScanCli	Runs repeatmasker on array designs.
ArrayDesignSequenceAssociationCli	Attach sequences to array design, fetching from BLAST database if requested.
ArrayDesignSequenceManipulatingCli	Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
ArrayDesignSubsumptionTesterCli	Test two array designs to see if one subsumes the other, and if so update their information.
BatchEffectPopulationCli	For bulk processing of batch-info-fetching.
BibRefUpdaterCli	Refreshes the information in all the bibliographic references in the system.
BioSequenceCleanupCli	Goes through the biosequences for array designs in the database and removes duplicates.
BlacklistCli	Add entries to the blacklist
CompleteCli	This CLI provide various runtime completions that can be re-used by other CLIs.
DatabaseViewGeneratorCLI	Simple driver of DatabaseViewGenerator.
DeleteDiffExCli	Delete differential expression analsyes on a per-experiment basis.
DeleteExperimentsCli	Delete one or more experiments from the system.
DetectQuantitationTypeCli
DifferentialExpressionAnalysisCli	A command line interface to the DifferentialExpressionAnalysis.
ExperimentalDesignImportCli
ExperimentalDesignViewCli
ExperimentalDesignWriterCLI	Writes out the experimental design for a given experiment.
ExpressionDataCorrMatCli	Create correlation visualizations for expression experiments
ExpressionDataMatrixWriterCLI	Prints preferred data matrix to a file.
ExpressionExperimentDataFileGeneratorCli
ExpressionExperimentDataUpdaterCli	Update GEO data for an experiment.
ExpressionExperimentManipulatingCLI	Base class for CLIs that needs one or more expression experiment as an input.
ExpressionExperimentMetadataChangelogEntryAdderCli	CLI tool for adding manual entries to the changelog file of an experiment.
ExpressionExperimentMetadataChangelogViewerCli	CLI tool for viewing the changelog file of an experiment.
ExpressionExperimentMetadataFileAdderCli	Add a metadata file to an experiment and record an entry in the changelog file.
ExpressionExperimentPlatformSwitchCli	Switch the array design used to the merged one.
ExpressionExperimentPrimaryPubCli	Update the primary publication for experiments.
ExpressionExperimentVectorsManipulatingCli<T extends DataVector>	Base class for CLI tools that manipulate expression experiment vectors.
ExternalDatabaseAdderCli	Add a new external database, but requires editing the code to do so.
ExternalDatabaseOverviewCli
ExternalDatabaseUpdaterCli
ExternalFileGeneLoaderCLI	CLI for loading genes from a non NCBI files.
FactorValueMigratorCLI	Deprecated. this will be removed as soon as all the old-style characteristics are migrated
FindObsoleteTermsCli
FixOntologyTermLabelsCli
GeeqCli	Generate or update GEEQ scores
GenerateDatabaseUpdateCli	Generate a database update script.
GenericGenelistDesignGenerator	Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
GeoGrabberCli	Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.
IndexGemmaCLI
InitializeDatabaseCli	Initialize the database.
LinkAnalysisCli	Commandline tool to conduct link (coexpression) analysis.
ListExpressionDataFIleLocksCli	List all locks within Gemma's data directories.
ListQuantitationTypesCli
LoadExpressionDataCli	Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.
LoadSimpleExpressionDataCli	Command Line tools for loading the expression experiment in flat files
LockExpressionDataFileCli	This CLI allows one to lock an experiment data or metadata file.
MakeExperimentPrivateCli
MakeExperimentsPublicCli	Make data sets public.
MeshTermFetcherCli	Deprecated. should not be part of Gemma main code
MultifunctionalityCli
NCBIGene2GOAssociationLoaderCLI	Load GO -> gene associations from NCBI.
NcbiGeneLoaderCLI	Command line interface to gene parsing and loading
OrderVectorsByDesignCli	Use to change the order of the values to match the experimental design.
ProcessedDataComputeCLI	Prepare the "processed" expression data vectors, and can also do batch correction.
ProcessedDataDeleterCli
ProtocolAdderCli
ProtocolDeleterCli
ProtocolListCli
PubMedLoaderCli	Load PubMed files from XML files -- not used routinely!
PubMedSearcher	Simple application to perform pubmed searches from a list of terms, and persist the results in the database.
RawDataDeleterCli
RawExpressionDataWriterCli
RefreshExperimentCli
ReplaceDataCli	Replace data in an existing data set.
RNASeqBatchInfoCli	Deprecated. this should not be necessary and the regular batch population tool can be used instead.
RNASeqDataAddCli	Designed to add count and/or RPKM data to a data set that has only meta-data.
SingleCellDataAggregateDeleterCli
SingleCellDataAggregatorCli
SingleCellDataDeleterCli
SingleCellDataDownloaderCli
SingleCellDataLoaderCli
SingleCellDataTransformCli	Transform various single-cell formats.
SingleCellDataWriterCli
SingleCellSparsityMetricsUpdaterCli
SplitExperimentCli	Split an experiment into parts based on an experimental factor
SVDCli
TaxonLoaderCli
UnifiedOntologyUpdaterCli
UpdateDatabaseCli	Update the database.
UpdateEe2AdCli
UpdateEE2CCli
UpdateGene2CsCli
UpdatePubMedCli	Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.
VectorMergingCli	For experiments that used multiple array designs, merge the expression profiles