.env.example
.gitignore
.pre-commit-config.yaml
CONTRIBUTING.md
Dockerfile
LICENSE
Makefile
README.md
dev_install.sh
install-ubuntu.sh
install.bat
install.ps1
main.py
pyproject.toml
pytest.ini
setup.py
verify_installation.py
lobster/__init__.py
lobster/__main__.py
lobster/_version.py
lobster/cli.py
lobster/main.py
lobster/version.py
lobster/agents/__init__.py
lobster/agents/bulk_rnaseq_expert.py
lobster/agents/data_expert.py
lobster/agents/data_expert_assistant.py
lobster/agents/draw_graph.py
lobster/agents/graph.py
lobster/agents/machine_learning_expert.py
lobster/agents/metadata_assistant.py
lobster/agents/protein_structure_visualization_expert.py
lobster/agents/research_agent.py
lobster/agents/singlecell_expert.py
lobster/agents/state.py
lobster/agents/supervisor.py
lobster/agents/visualization_expert.py
lobster/agents/archive/ARCHIVE_NOTICE.md
lobster/agents/archive/research_agent_assistant.py
lobster/agents/langgraph_supervisor/__init__.py
lobster/agents/langgraph_supervisor/agent_name.py
lobster/agents/langgraph_supervisor/handoff.py
lobster/agents/langgraph_supervisor/supervisor.py
lobster/config/README_CONFIGURATION.md
lobster/config/README_THINKING.md
lobster/config/__init__.py
lobster/config/agent_capabilities.py
lobster/config/agent_config.py
lobster/config/agent_registry.py
lobster/config/config_manager.py
lobster/config/llm_factory.py
lobster/config/settings.py
lobster/config/supervisor_config.py
lobster/core/__init__.py
lobster/core/analysis_ir.py
lobster/core/archive_utils.py
lobster/core/client.py
lobster/core/data_manager_v2.py
lobster/core/download_queue.py
lobster/core/exceptions.py
lobster/core/extraction_cache.py
lobster/core/ir_coverage.py
lobster/core/notebook_executor.py
lobster/core/notebook_exporter.py
lobster/core/notebook_validator.py
lobster/core/provenance.py
lobster/core/adapters/__init__.py
lobster/core/adapters/base.py
lobster/core/adapters/protein_structure_adapter.py
lobster/core/adapters/pseudobulk_adapter.py
lobster/core/adapters/transcriptomics_adapter.py
lobster/core/backends/__init__.py
lobster/core/backends/base.py
lobster/core/backends/h5ad_backend.py
lobster/core/backends/mudata_backend.py
lobster/core/interfaces/__init__.py
lobster/core/interfaces/adapter.py
lobster/core/interfaces/backend.py
lobster/core/interfaces/base_client.py
lobster/core/interfaces/validator.py
lobster/core/schemas/__init__.py
lobster/core/schemas/database_mappings.py
lobster/core/schemas/download_queue.py
lobster/core/schemas/protein_structure.py
lobster/core/schemas/transcriptomics.py
lobster/core/schemas/validation.py
lobster/core/utils/__init__.py
lobster/core/utils/h5ad_utils.py
lobster/lobster_cloud/__init__.py
lobster/lobster_cloud/client.py
lobster/tools/__init__.py
lobster/tools/annotation_templates.py
lobster/tools/bulk_rnaseq_service.py
lobster/tools/clustering_service.py
lobster/tools/concatenation_service.py
lobster/tools/content_access_service.py
lobster/tools/differential_formula_service.py
lobster/tools/docling_service.py
lobster/tools/enhanced_handoff_tool.py
lobster/tools/enhanced_singlecell_service.py
lobster/tools/expert_handoff_manager.py
lobster/tools/expert_handoff_patterns.py
lobster/tools/geo_downloader.py
lobster/tools/geo_fallback_service.py
lobster/tools/geo_parser.py
lobster/tools/geo_service.py
lobster/tools/gpu_detector.py
lobster/tools/handoff_tool.py
lobster/tools/manual_annotation_service.py
lobster/tools/metadata_standardization_service.py
lobster/tools/metadata_validation_service.py
lobster/tools/pipeline_strategy.py
lobster/tools/preprocessing_service.py
lobster/tools/protein_structure_fetch_service.py
lobster/tools/pseudobulk_service.py
lobster/tools/pymol_visualization_service.py
lobster/tools/quality_service.py
lobster/tools/rate_limiter.py
lobster/tools/sample_mapping_service.py
lobster/tools/scvi_embedding_service.py
lobster/tools/structure_analysis_service.py
lobster/tools/visualization_service.py
lobster/tools/workflow_tracker.py
lobster/tools/workspace_content_service.py
lobster/tools/workspace_tool.py
lobster/tools/archive/MIGRATION_NOTICE.md
lobster/tools/archive/publication_service.py
lobster/tools/archive/unified_content_service.py
lobster/tools/external_providers_context/chimerax_tut.md
lobster/tools/providers/__init__.py
lobster/tools/providers/abstract_provider.py
lobster/tools/providers/base_provider.py
lobster/tools/providers/biopython_entrez_wrapper.py
lobster/tools/providers/geo_provider.py
lobster/tools/providers/geo_utils.py
lobster/tools/providers/ncbi_query_builder.py
lobster/tools/providers/organism_enum.py
lobster/tools/providers/pdb_provider.py
lobster/tools/providers/pmc_provider.py
lobster/tools/providers/provider_registry.py
lobster/tools/providers/publication_resolver.py
lobster/tools/providers/pubmed_provider.py
lobster/tools/providers/sra_provider.py
lobster/tools/providers/structure_provider.py
lobster/tools/providers/webpage_provider.py
lobster/ui/__init__.py
lobster/ui/console_manager.py
lobster/ui/live_dashboard.py
lobster/ui/progress_manager.py
lobster/ui/themes.py
lobster/ui/components/__init__.py
lobster/ui/components/file_tree.py
lobster/ui/components/multi_progress.py
lobster/ui/components/status_display.py
lobster/ui/formatters/__init__.py
lobster/utils/__init__.py
lobster/utils/callbacks.py
lobster/utils/error_handlers.py
lobster/utils/file_analyzer.py
lobster/utils/file_naming.py
lobster/utils/json_extractor.py
lobster/utils/logger.py
lobster/utils/progress_wrapper.py
lobster/utils/ssl_utils.py
lobster/utils/system.py
lobster_ai.egg-info/PKG-INFO
lobster_ai.egg-info/SOURCES.txt
lobster_ai.egg-info/dependency_links.txt
lobster_ai.egg-info/entry_points.txt
lobster_ai.egg-info/requires.txt
lobster_ai.egg-info/top_level.txt