- AbstractCLI
- AbstractCLIContextCLI
- AbstractSpringAwareCLI
- AffyDataFromCelCli
- AffyProbeCollapseCli
- ArrayDesignAlternativePopulateCli
- ArrayDesignAnnotationFileCli
- ArrayDesignAuditTrailCleanupCli
- ArrayDesignBioSequenceDetachCli
- ArrayDesignBlatCli
- ArrayDesignMapSummaryCli
- ArrayDesignMergeCli
- ArrayDesignProbeCleanupCLI
- ArrayDesignProbeMapperCli
- ArrayDesignProbeRenamerCli
- ArrayDesignRepeatScanCli
- ArrayDesignSequenceAssociationCli
- ArrayDesignSequenceManipulatingCli
- ArrayDesignSubsumptionTesterCli
- BatchEffectPopulationCli
- BibRefUpdaterCli
- BioSequenceCleanupCli
- BlacklistCli
- CLI
- CountObsoleteTermsCli
- CtdDatabaseImporterCli
- DatabaseViewGeneratorCLI
- DeleteDiffExCli
- DeleteEvidenceCLI
- DeleteExperimentsCli
- DgaDatabaseImporterCli
- DifferentialExpressionAnalysisCli
- EvidenceImporterAbstractCLI
- EvidenceImporterCLI
- ExperimentalDesignImportCli
- ExperimentalDesignViewCli
- ExperimentalDesignWriterCLI
- ExpressionDataCorrMatCli
- ExpressionDataMatrixWriterCLI
- ExpressionExperimentDataFileGeneratorCli
- ExpressionExperimentManipulatingCLI
- ExpressionExperimentPlatformSwitchCli
- ExpressionExperimentPrimaryPubCli
- ExternalDatabaseAdderCli
- ExternalDatabaseEvidenceImporterAbstractCLI
- ExternalDatabaseUpdaterCli
- ExternalFileGeneLoaderCLI
- GeeqCli
- GemmaCLI
- GemmaCLI.CommandGroup
- GenericGenelistDesignGenerator
- GeoGrabberCli
- GwasDatabaseImporterCli
- IndexGemmaCLI
- LinkAnalysisCli
- LoadEvidenceForClassifier
- LoadExpressionDataCli
- LoadSimpleExpressionDataCli
- MakeExperimentsPublicCli
- MeshTermFetcherCli
- MultifunctionalityCli
- NCBIGene2GOAssociationLoaderCLI
- NcbiGeneLoaderCLI
- OmimDatabaseImporterCli
- OrderVectorsByDesignCli
- ProcessedDataComputeCLI
- PubMedLoaderCli
- PubMedSearcher
- ReplaceDataCli
- RgdDatabaseImporterCli
- RNASeqBatchInfoCli
- RNASeqDataAddCli
- SfariDatabaseImporterCli
- SplitExperimentCli
- SVDCli
- TaxonLoaderCli
- TwoChannelMissingValueCLI
- UpdatePubMedCli
- VectorMergingCli