├── .gitattributes ├── .gitignore ├── Documentation ├── Examples │ └── example1_getting-started │ │ ├── EDT.csv │ │ ├── Layout.csv │ │ ├── analyse_qc │ │ ├── p1_ammonium.pdf │ │ ├── p2_valine.pdf │ │ ├── p3_glycine.pdf │ │ └── p4_arginine.pdf │ │ ├── commands.txt │ │ ├── images │ │ ├── p1.jpg │ │ ├── p2.jpg │ │ ├── p3.jpg │ │ └── p4.jpg │ │ ├── pyphe-analyse_data_report.csv │ │ ├── pyphe-quantify-report_reps.csv │ │ ├── pyphe-quantify-report_summaryStats.csv │ │ ├── pyphe_quant │ │ ├── p1.jpg.csv │ │ ├── p2.jpg.csv │ │ ├── p3.jpg.csv │ │ └── p4.jpg.csv │ │ └── qc_images │ │ ├── qc_p1.jpg.png │ │ ├── qc_p2.jpg.png │ │ ├── qc_p3.jpg.png │ │ └── qc_p4.jpg.png ├── Growthcurves │ ├── example_data.csv │ ├── example_data_curves.pdf │ └── example_data_results.csv └── Scan │ ├── cuttingVectors_fixture_petrieDishes.svg │ └── cuttingVectors_fixture_som3.svg ├── LICENSE ├── README.md ├── bin ├── pyphe-analyse ├── pyphe-analyse-gui ├── pyphe-analyse.bat ├── pyphe-growthcurves ├── pyphe-growthcurves.bat ├── pyphe-interpret ├── pyphe-interpret.bat ├── pyphe-quantify ├── pyphe-quantify.bat ├── pyphe-scan └── pyphe-scan-timecourse ├── icons ├── gui.png ├── toolbox-72dpi_tp.png ├── toolbox-72dpi_white.png └── toolbox_icon-01.png ├── pyphe ├── __init__.py ├── __pycache__ │ └── quantify.cpython-37.pyc ├── analysis.py ├── growthcurves.py ├── interpret.py ├── quantify.py └── scan.py ├── setup.py └── test ├── edt.csv ├── example-pipeline.bat ├── example-pipeline.sh ├── images ├── p1_53.jpg ├── p1_72.jpg ├── p1_91.jpg └── timepoints.txt ├── layout_wide.csv ├── pyphe-analyse_data_report.csv ├── pyphe-quantify-report_reps.csv ├── pyphe-quantify-report_summaryStats.csv ├── pyphe_quant ├── p1_53.jpg.csv ├── p1_72.jpg.csv └── p1_91.jpg.csv ├── qc_images ├── qc_p1_53.jpg.png ├── qc_p1_72.jpg.png └── qc_p1_91.jpg.png └── timecourse_quant └── p1_91.jpg.csv /.gitattributes: -------------------------------------------------------------------------------- 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