README.md
setup.py
CASSIA/CASSIA_python_tutorial.py
CASSIA/LLM_evaluation_getscore.py
CASSIA/LLM_evaluation_test.py
CASSIA/__init__.py
CASSIA/generate_comparison.py
CASSIA/run_full_test.py
CASSIA.egg-info/PKG-INFO
CASSIA.egg-info/SOURCES.txt
CASSIA.egg-info/dependency_links.txt
CASSIA.egg-info/requires.txt
CASSIA.egg-info/top_level.txt
CASSIA/agents/__init__.py
CASSIA/agents/annotation_boost/__init__.py
CASSIA/agents/annotation_boost/annotation_boost.py
CASSIA/agents/annotation_boost/super_annotation_boost.py
CASSIA/agents/merging/__init__.py
CASSIA/agents/merging/merging_annotation.py
CASSIA/agents/reference_agent/__init__.py
CASSIA/agents/reference_agent/complexity_scorer.py
CASSIA/agents/reference_agent/reference_agent.py
CASSIA/agents/reference_agent/reference_selector.py
CASSIA/agents/reference_agent/section_extractor.py
CASSIA/agents/reference_agent/utils.py
CASSIA/agents/subclustering/__init__.py
CASSIA/agents/subclustering/subclustering.py
CASSIA/agents/uncertainty/Uncertainty_quantification.py
CASSIA/agents/uncertainty/__init__.py
CASSIA/comparison/__init__.py
CASSIA/comparison/symphony_compare.py
CASSIA/config/__init__.py
CASSIA/core/__init__.py
CASSIA/core/anndata_utils.py
CASSIA/core/api_validation.py
CASSIA/core/exceptions.py
CASSIA/core/free_api.py
CASSIA/core/gene_id_converter.py
CASSIA/core/llm_utils.py
CASSIA/core/logging_config.py
CASSIA/core/marker_utils.py
CASSIA/core/model_settings.py
CASSIA/core/progress_tracker.py
CASSIA/core/proxy_config.py
CASSIA/core/utils.py
CASSIA/core/validation.py
CASSIA/data/CASSIA_Package_Documentation.md
CASSIA/data/README_model_settings.md
CASSIA/data/__init__.py
CASSIA/data/model_settings.json
CASSIA/data/processed.csv
CASSIA/data/subcluster_results.csv
CASSIA/data/unprocessed.csv
CASSIA/engine/__init__.py
CASSIA/engine/main_function_code.py
CASSIA/engine/tools_function.py
CASSIA/evaluation/LLM_evaluation.py
CASSIA/evaluation/__init__.py
CASSIA/evaluation/cell_type_comparison.py
CASSIA/evaluation/scoring.py
CASSIA/hypothesis/__init__.py
CASSIA/hypothesis/hypothesis_generation.py
CASSIA/hypothesis/summarize_hypothesis_runs.py
CASSIA/imaging/__init__.py
CASSIA/imaging/llm_image.py
CASSIA/pipeline/__init__.py
CASSIA/pipeline/pipeline.py
CASSIA/reports/__init__.py
CASSIA/reports/generate_batch_report.py
CASSIA/reports/generate_hypothesis_report.py
CASSIA/reports/generate_report_uncertainty.py
CASSIA/reports/generate_reports.py