├── AutoFlow Step by Step.md ├── BioLLM Comparision.ipynb ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Code Evaluation of Static Task Examples.md ├── Code Generation of Static Task Examples.md ├── Dynamic Execution of Level 1 Tasks.md ├── Dynamic Execution of Level 2 Tasks.md ├── Dynamic Execution of Level 3 Tasks.md ├── Environment_Configuration.csv ├── LICENSE ├── OmixBenchR ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── OmixBenchR.Rproj ├── R │ ├── CodeEval.R │ ├── Execute_Task.R │ ├── Execute_Tasks.R │ └── bioinfo_prompt_formatter.R ├── inst │ └── Bioinformatics Code Static Evaluation Prompt.md └── man │ ├── CodeEval.Rd │ ├── Execute_Task.Rd │ ├── Execute_Tasks.Rd │ └── bioinfo_prompt_formatter.Rd ├── OmixBenchR_1.0.0.pdf ├── OmixBenchR_1.0.0.tar.gz ├── OmixQA ├── DynamicEval.R ├── OmixQA-Task-Info.xlsx ├── OmixQA_Distribution.R ├── OmixQA_Distribution.pdf └── OmixQA_Distribution2.pdf ├── OmixStaticEval_Py.ipynb ├── OmixTask1002 ├── CorWithHuman.pdf ├── Correlation.R ├── Eval-Cor-Human.xlsx ├── OmixTask1002.xlsx ├── OmixTask1002_Distribution.pdf ├── Task_Distribution.R ├── WordCloud.pdf └── ~$OmixTask1002.xlsx ├── README.md ├── SECURITY.md ├── StaticEval ├── Bioinformatics Code Static Evaluation Prompt.md ├── Qwen_parameter_vs_performance.R ├── Qwen_parameter_vs_performance.pdf ├── StaticEval.R ├── Thinking_Mode_vs_performance.R ├── Thinking_Mode_vs_performance.pdf ├── eval_final.csv ├── forheatmap.csv ├── heatmap.R ├── heatmap.pdf ├── heatmap.png ├── llm_parameter_vs_performance.pdf ├── radar-rank.pdf ├── ranker.R └── regression.R ├── Task Complexity Classification.md ├── llmflow ├── AutoFlow_Tasks.R ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R │ ├── AutoFlow.R │ ├── extract_chat_history.R │ ├── extract_code.R │ ├── extract_json.R │ ├── extract_package_info.R │ ├── extraction.R │ ├── generate_qa_from_docs.R │ ├── prompt_from_history.R │ ├── react.R │ ├── response_as_json.R │ ├── response_to_r.R │ └── utils.R ├── llmflow.Rproj └── man │ ├── AutoFlow.Rd │ ├── extract_bash_code.Rd │ ├── extract_chat_history.Rd │ ├── extract_code.Rd │ ├── extract_docs_from_tarball.Rd │ ├── extract_function_docs.Rd │ ├── extract_function_examples.Rd │ ├── extract_javascript_code.Rd │ ├── extract_json.Rd │ ├── extract_package_docs.Rd │ ├── extract_python_code.Rd │ ├── extract_r_code.Rd │ ├── extract_sql_code.Rd │ ├── generate_qa_from_docs.Rd │ ├── hello.Rd │ ├── package_extraction_prompt.Rd │ ├── package_function_schema.Rd │ ├── prompt_from_history.Rd │ ├── react_r.Rd │ ├── react_using_r.Rd │ ├── response_as_json.Rd │ ├── response_to_r.Rd │ ├── retrieve_docs.Rd │ └── save_code_to_file.Rd ├── llmflow_2.0.0.pdf ├── llmflow_2.0.0.tar.gz ├── llmhelper ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── build_prompt.R │ ├── get_llm_response.R │ ├── json_schema.R │ ├── llm_client.R │ ├── ollama.R │ ├── prompt.R │ ├── swagger_api_to_docs.R │ └── utils.R ├── llmhelper.Rproj └── man │ ├── build_prompt.Rd │ ├── 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