CHANGELOG.md
LICENSE
MANIFEST.in
README.md
celltypeAgent_config.json
manage.py
pyproject.toml
requirements.txt
setup.py
celltypeAgent/__init__.py
celltypeAgent/celltypeAgent_config.json
celltypeAgent/servers.py
celltypeAgent/api/__init__.py
celltypeAgent/api/annotation.py
celltypeAgent/api/celltype_analysis.py
celltypeAgent/api/data_processing.py
celltypeAgent/api/main_workflow.py
celltypeAgent/appagent/__init__.py
celltypeAgent/appagent/example_usage.py
celltypeAgent/appagent/mcp_client_example.py
celltypeAgent/appagent/agent/__init__.py
celltypeAgent/appagent/agent/celltype_annotation_agent.py
celltypeAgent/appagent/api/main.py
celltypeAgent/appagent/api/models.py
celltypeAgent/appagent/api/routes.py
celltypeAgent/appagent/api/service.py
celltypeAgent/appagent/clients/__init__.py
celltypeAgent/appagent/clients/mcp_client.py
celltypeAgent/appagent/config/__init__.py
celltypeAgent/appagent/config/cache_config.py
celltypeAgent/appagent/config/prompts.py
celltypeAgent/appagent/config/settings.py
celltypeAgent/appagent/llm/__init__.py
celltypeAgent/appagent/locales/en_US.json
celltypeAgent/appagent/locales/zh_CN.json
celltypeAgent/appagent/services/__init__.py
celltypeAgent/appagent/services/mcp_server.py
celltypeAgent/appagent/tools/celldex_download_tool.py
celltypeAgent/appagent/tools/celldex_info_tool.py
celltypeAgent/appagent/tools/celltypist_simple.py
celltypeAgent/appagent/tools/file_validators.py
celltypeAgent/appagent/tools/get_celldex_projects_bilingual.py
celltypeAgent/appagent/tools/get_celltypist_models.py
celltypeAgent/appagent/tools/get_sctype_tissues.py
celltypeAgent/appagent/tools/run_sctype_test.py
celltypeAgent/appagent/tools/sctype_simple.py
celltypeAgent/appagent/tools/singleR_simple.py
celltypeAgent/appagent/tools/species_detection.py
celltypeAgent/appagent/tools/test_file_format_fallback.py
celltypeAgent/appagent/tools/r/__init__.py
celltypeAgent/appagent/tools/r/sctype_run.R
celltypeAgent/appagent/tools/r/sctype/ScTypeDB_full.xlsx
celltypeAgent/appagent/tools/r/sctype/__init__.py
celltypeAgent/appagent/tools/r/sctype/auto_detect_tissue_type.R
celltypeAgent/appagent/tools/r/sctype/gene_sets_prepare.R
celltypeAgent/appagent/tools/r/sctype/sctype_score_.R
celltypeAgent/appagent/tools/r/sctype/sctype_wrapper.R
celltypeAgent/appagent/utils/__init__.py
celltypeAgent/appagent/utils/common.py
celltypeAgent/appagent/utils/content_processor.py
celltypeAgent/appagent/utils/i18n.py
celltypeAgent/appagent/utils/output_logger.py
celltypeAgent/appagent/utils/parser.py
celltypeAgent/appagent/utils/path_manager copy.py
celltypeAgent/appagent/utils/path_manager.py
celltypeAgent/appagent/utils/validator.py
celltypeAgent/common/__init__.py
celltypeAgent/common/base_content_processor.py
celltypeAgent/common/base_parser.py
celltypeAgent/common/base_validator.py
celltypeAgent/common/llm_client.py
celltypeAgent/common/llm_logger.py
celltypeAgent/common/log_token_parser.py
celltypeAgent/common/streaming_filter.py
celltypeAgent/common/token_statistics.py
celltypeAgent/config/__init__.py
celltypeAgent/config/global_config.py
celltypeAgent/config/paths_config.py
celltypeAgent/config/unified_logger.py
celltypeAgent/dataagent/__init__.py
celltypeAgent/dataagent/api_usage_example.py
celltypeAgent/dataagent/mcp_client_example.py
celltypeAgent/dataagent/agent/__init__.py
celltypeAgent/dataagent/agent/data_processor_agent.py
celltypeAgent/dataagent/api/__init__.py
celltypeAgent/dataagent/api/rest_server.py
celltypeAgent/dataagent/clients/__init__.py
celltypeAgent/dataagent/clients/mcp_client.py
celltypeAgent/dataagent/config/__init__.py
celltypeAgent/dataagent/config/cache_config.py
celltypeAgent/dataagent/config/prompts.py
celltypeAgent/dataagent/config/settings.py
celltypeAgent/dataagent/llm/__init__.py
celltypeAgent/dataagent/locales/en_US.json
celltypeAgent/dataagent/locales/zh_CN.json
celltypeAgent/dataagent/services/mcp_server.py
celltypeAgent/dataagent/tools/data_converters.py
celltypeAgent/dataagent/tools/filetool.py
celltypeAgent/dataagent/tools/save_marker_genes.py
celltypeAgent/dataagent/tools/save_marker_genes_r.R
celltypeAgent/dataagent/utils/__init__.py
celltypeAgent/dataagent/utils/common.py
celltypeAgent/dataagent/utils/content_processor.py
celltypeAgent/dataagent/utils/i18n.py
celltypeAgent/dataagent/utils/output_logger.py
celltypeAgent/dataagent/utils/parser.py
celltypeAgent/dataagent/utils/path_manager.py
celltypeAgent/dataagent/utils/path_normalizer.py
celltypeAgent/dataagent/utils/validator.py
celltypeAgent/examples/app_example.py
celltypeAgent/examples/data_example.py
celltypeAgent/examples/main_example.py
celltypeAgent/examples/run_all_examples.py
celltypeAgent/examples/subagent_example.py
celltypeAgent/mainagent/__init__.py
celltypeAgent/mainagent/celltypeAgent_config.json
celltypeAgent/mainagent/main_agent.py
celltypeAgent/mainagent/mcp_client_example.py
celltypeAgent/mainagent/agent/__init__.py
celltypeAgent/mainagent/agent/main_react_agent.py
celltypeAgent/mainagent/clients/__init__.py
celltypeAgent/mainagent/clients/mcp_client.py
celltypeAgent/mainagent/clients/subagent_client.py
celltypeAgent/mainagent/config/__init__.py
celltypeAgent/mainagent/config/cache_config.py
celltypeAgent/mainagent/config/prompts.py
celltypeAgent/mainagent/config/session_config.py
celltypeAgent/mainagent/config/settings.py
celltypeAgent/mainagent/llm/__init__.py
celltypeAgent/mainagent/locales/en_US.json
celltypeAgent/mainagent/locales/zh_CN.json
celltypeAgent/mainagent/services/mcp_server.py
celltypeAgent/mainagent/tools/__init__.py
celltypeAgent/mainagent/tools/adata_mapping.py
celltypeAgent/mainagent/tools/cluster_tools.py
celltypeAgent/mainagent/tools/file_paths_tools.py
celltypeAgent/mainagent/tools/mapping_tools.py
celltypeAgent/mainagent/tools/subagent_tools.py
celltypeAgent/mainagent/utils/__init__.py
celltypeAgent/mainagent/utils/content_processor.py
celltypeAgent/mainagent/utils/i18n.py
celltypeAgent/mainagent/utils/output_logger.py
celltypeAgent/mainagent/utils/parser.py
celltypeAgent/mainagent/utils/path_manager.py
celltypeAgent/mainagent/utils/validator.py
celltypeAgent/subagent/__init__.py
celltypeAgent/subagent/analyze_clusters_from_csv.py
celltypeAgent/subagent/api_usage_example.py
celltypeAgent/subagent/mcp_client_example.py
celltypeAgent/subagent/.celltype_cache/cellmarker/cellmarker_merged_all.json
celltypeAgent/subagent/.celltype_cache/ncbi/human_gene_mapping.json
celltypeAgent/subagent/.celltype_cache/ncbi/mouse_gene_mapping.json
celltypeAgent/subagent/.celltype_cache/panglaodb/panglaodb_markers.json
celltypeAgent/subagent/agent/__init__.py
celltypeAgent/subagent/agent/celltype_react_agent.py
celltypeAgent/subagent/api/main.py
celltypeAgent/subagent/api/models.py
celltypeAgent/subagent/api/routes.py
celltypeAgent/subagent/api/service.py
celltypeAgent/subagent/clients/__init__.py
celltypeAgent/subagent/clients/mcp_client.py
celltypeAgent/subagent/config/__init__.py
celltypeAgent/subagent/config/cache_config.py
celltypeAgent/subagent/config/prompts.py
celltypeAgent/subagent/config/settings.py
celltypeAgent/subagent/llm/__init__.py
celltypeAgent/subagent/llm/logger.py
celltypeAgent/subagent/locales/en_US.json
celltypeAgent/subagent/locales/zh_CN.json
celltypeAgent/subagent/services/mcp_server.py
celltypeAgent/subagent/services/rest_api_server.py
celltypeAgent/subagent/tools/__init__.py
celltypeAgent/subagent/tools/analysis/__init__.py
celltypeAgent/subagent/tools/analysis/gene_enrichment.py
celltypeAgent/subagent/tools/fetchers/__init__.py
celltypeAgent/subagent/tools/fetchers/cellmarker_fetcher.py
celltypeAgent/subagent/tools/fetchers/panglaodb_fetcher.py
celltypeAgent/subagent/tools/ncbi/__init__.py
celltypeAgent/subagent/tools/ncbi/gene_info_manager.py
celltypeAgent/subagent/tools/ncbi/ncbi_api_adapter.py
celltypeAgent/subagent/utils/__init__.py
celltypeAgent/subagent/utils/common.py
celltypeAgent/subagent/utils/content_processor.py
celltypeAgent/subagent/utils/file_utils.py
celltypeAgent/subagent/utils/i18n.py
celltypeAgent/subagent/utils/output_logger.py
celltypeAgent/subagent/utils/output_logger_streaming_backup.py
celltypeAgent/subagent/utils/parser.py
celltypeAgent/subagent/utils/path_manager.py
celltypeAgent/subagent/utils/validator.py