├── .DS_Store ├── Pipeline_K50_dG ├── .DS_Store ├── .ipynb_checkpoints │ ├── STEP1_run-checkpoint.ipynb │ ├── STEP2_run-checkpoint.ipynb │ ├── STEP3_run-checkpoint.ipynb │ ├── STEP4_module-checkpoint.ipynb │ ├── STEP4_run-checkpoint.ipynb │ ├── STEP5_module-checkpoint.ipynb │ └── STEP5_run-checkpoint.ipynb ├── Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib2.csv ├── Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib4.csv ├── Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib3.csv ├── Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib4.csv ├── Raw_NGS_counts_overlapped_seqs_STEP1_lib3_lib4.csv ├── STEP1_module.ipynb ├── STEP1_module.py ├── STEP1_out_protease_concentration_chymotrypsin ├── STEP1_out_protease_concentration_trypsin ├── STEP1_run.ipynb ├── STEP2_run.ipynb ├── STEP3_run.ipynb ├── STEP4_module.ipynb ├── STEP4_run.ipynb ├── STEP5_module.ipynb └── STEP5_run.ipynb ├── Pipeline_figure_model ├── .ipynb_checkpoints │ ├── Additive_model_Fig4-checkpoint.ipynb │ ├── 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