LICENSE
pyproject.toml
geneprep/environment.py
geneprep/eval.py
geneprep/main.py
geneprep/test_data.py
geneprep/test_environment.py
geneprep.egg-info/PKG-INFO
geneprep.egg-info/SOURCES.txt
geneprep.egg-info/dependency_links.txt
geneprep.egg-info/requires.txt
geneprep.egg-info/top_level.txt
geneprep/agents/__init__.py
geneprep/agents/base_agent.py
geneprep/agents/code_reviewer.py
geneprep/agents/domain_expert.py
geneprep/agents/geo_agent.py
geneprep/agents/multi_step_agent.py
geneprep/agents/pi_agent.py
geneprep/agents/statistician_agent.py
geneprep/agents/tcga_agent.py
geneprep/core/__init__.py
geneprep/core/context.py
geneprep/core/execution.py
geneprep/core/messaging.py
geneprep/download/download_GEO_data.py
geneprep/download/get_gene_synonyms.py
geneprep/download/get_opentargets_genes.py
geneprep/download/validator.py
geneprep/examples/regress.py
geneprep/examples/preprocess/GSE153316.py
geneprep/examples/preprocess/GSE207847.py
geneprep/examples/preprocess/GSE208101.py
geneprep/examples/preprocess/GSE225328.py
geneprep/examples/preprocess/GSE234017.py
geneprep/examples/preprocess/GSE236725.py
geneprep/examples/preprocess/GSE248830.py
geneprep/examples/preprocess/GSE249377.py
geneprep/examples/preprocess/GSE270721.py
geneprep/examples/preprocess/GSE283522.py
geneprep/examples/preprocess/TCGA.py
geneprep/metadata/gene_synonym.json
geneprep/metadata/task_info.json
geneprep/output/preprocess/1/Acute_Myeloid_Leukemia/code/TCGA.py
geneprep/output/preprocess/1/Bladder_Cancer/code/TCGA.py
geneprep/output/preprocess/1/Cervical_Cancer/code/TCGA.py
geneprep/output/preprocess/1/Glioblastoma/code/TCGA.py
geneprep/output/preprocess/1/Hypertension/code/TCGA.py
geneprep/output/preprocess/1/Pancreatic_Cancer/code/TCGA.py
geneprep/output/preprocess/1/Type_2_Diabetes/code/TCGA.py
geneprep/prompts/GEO.py
geneprep/prompts/TCGA.py
geneprep/prompts/__init__.py
geneprep/prompts/shared.py
geneprep/prompts/statistics.py
geneprep/tools/preprocess.py
geneprep/tools/statistics.py
geneprep/utils/__init__.py
geneprep/utils/config.py
geneprep/utils/config_ori.py
geneprep/utils/llm.py
geneprep/utils/llm_ori.py
geneprep/utils/logger.py
geneprep/utils/path_config.py
geneprep/utils/resource_monitor.py
geneprep/utils/utils.py