All Classes
- AbstractAuthenticatedCLI
- AbstractAutoSeekingCLI
- AbstractCLI
- AbstractCompletionGenerator
- AbstractDelegatingExecutorService
- AffyDataFromCelCli
- AffyProbeCollapseCli
- ArrayDesignAlternativePopulateCli
- ArrayDesignAnnotationFileCli
- ArrayDesignAuditTrailCleanupCli
- ArrayDesignBioSequenceDetachCli
- ArrayDesignBlatCli
- ArrayDesignMapSummaryCli
- ArrayDesignMergeCli
- ArrayDesignProbeCleanupCLI
- ArrayDesignProbeMapperCli
- ArrayDesignProbeRenamerCli
- ArrayDesignRepeatScanCli
- ArrayDesignSequenceAssociationCli
- ArrayDesignSequenceManipulatingCli
- ArrayDesignSubsumptionTesterCli
- BashCompletionGenerator
- BatchEffectPopulationCli
- BatchTaskExecutorService
- BatchTaskProcessingResult
- BatchTaskProgressReporter
- BatchTaskSummaryWriter
- BibRefUpdaterCli
- BioSequenceCleanupCli
- BlacklistCli
- CLI
- CLI.CommandGroup
- CLIAuthenticationAware
- CLIAuthenticationManager
- CliContext
- CompleteCli
- CompletionGenerator
- CompletionSource
- CompletionSource.Completion
- CompletionType
- CompletionUtils
- CompositeBatchTaskSummaryWriter
- ConfigurationLinter
- DatabaseViewGeneratorCLI
- DeleteDiffExCli
- DeleteExperimentsCli
- DetectQuantitationTypeCli
- DifferentialExpressionAnalysisCli
- EntityLocator
- EntityLocatorImpl
- EntityOptionsUtils
- EnumConverter
- EnumeratedByCommandConverter
- EnumeratedByCommandStringConverter
- EnumeratedConverter
- EnumeratedStringConverter
- ExperimentalDesignImportCli
- ExperimentalDesignViewCli
- ExperimentalDesignWriterCLI
- ExpressionDataCorrMatCli
- ExpressionDataMatrixWriterCLI
- ExpressionExperimentDataFileGeneratorCli
- ExpressionExperimentDataUpdaterCli
- ExpressionExperimentManipulatingCLI
- ExpressionExperimentMetadataChangelogEntryAdderCli
- ExpressionExperimentMetadataChangelogViewerCli
- ExpressionExperimentMetadataFileAdderCli
- ExpressionExperimentPlatformSwitchCli
- ExpressionExperimentPrimaryPubCli
- ExpressionExperimentVectorsManipulatingCli
- ExternalDatabaseAdderCli
- ExternalDatabaseOverviewCli
- ExternalDatabaseUpdaterCli
- ExternalFileGeneLoaderCLI
- FactorValueMigratorCLI
- FileUtils
- FindObsoleteTermsCli
- FishCompletionGenerator
- FixOntologyTermLabelsCli
- GeeqCli
- GemmaCLI
- GemmaRestApiClientAuthenticator
- GemmaRestApiClientConfig
- GenerateDatabaseUpdateCli
- GenericGenelistDesignGenerator
- GeoGrabberCli
- HelpUtils
- IndexGemmaCLI
- InitializeDatabaseCli
- LinkAnalysisCli
- ListExpressionDataFIleLocksCli
- ListQuantitationTypesCli
- LoadExpressionDataCli
- LoadSimpleExpressionDataCli
- LockExpressionDataFileCli
- Log4jConfigurer
- LoggerCompletionSource
- LoggingBatchTaskSummaryWriter
- LoggingConfigurer
- MakeExperimentPrivateCli
- MakeExperimentsPublicCli
- MeshTermFetcherCli
- MeterRegistryCliConfigurer
- MultifunctionalityCli
- NCBIGene2GOAssociationLoaderCLI
- NcbiGeneLoaderCLI
- OptionsUtils
- OrderVectorsByDesignCli
- ProcessedDataComputeCLI
- ProcessedDataDeleterCli
- ProtocolAdderCli
- ProtocolDeleterCli
- ProtocolListCli
- PrototypeScopeResolver
- PubMedLoaderCli
- PubMedSearcher
- RawDataDeleterCli
- RawExpressionDataWriterCli
- RefreshExperimentCli
- ReplaceDataCli
- RNASeqBatchInfoCli
- RNASeqDataAddCli
- SettingsCompletionSource
- ShellUtils
- SingleCellDataAggregateDeleterCli
- SingleCellDataAggregatorCli
- SingleCellDataDeleterCli
- SingleCellDataDownloaderCli
- SingleCellDataLoaderCli
- SingleCellDataTransformCli
- SingleCellDataWriterCli
- SingleCellSparsityMetricsUpdaterCli
- SplitExperimentCli
- SuppressBatchTaskSummaryWriter
- SVDCli
- SystemCliContext
- TaxonLoaderCli
- TextBatchTaskSummaryWriter
- TsvBatchTaskSummaryWriter
- UnifiedOntologyUpdaterCli
- UpdateDatabaseCli
- UpdateEe2AdCli
- UpdateEE2CCli
- UpdateGene2CsCli
- UpdatePubMedCli
- VectorMergingCli