├── .gitignore ├── LICENSE ├── README.md ├── examples ├── Example_1_GI_network_doxorubicin.ipynb ├── Example_2_New_network_GO.ipynb └── Example_3_Scatterplot_annotation.ipynb ├── extras └── requirements.txt ├── safepy ├── __init__.py ├── run.py ├── safe.py ├── safe_colormaps.py ├── safe_default.ini ├── safe_extras.py ├── safe_io.py └── utils │ └── make_go.py └── tests ├── test_enrichments.py ├── test_imports.py └── test_neighborhoods.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/README.md -------------------------------------------------------------------------------- /examples/Example_1_GI_network_doxorubicin.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/examples/Example_1_GI_network_doxorubicin.ipynb -------------------------------------------------------------------------------- /examples/Example_2_New_network_GO.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/examples/Example_2_New_network_GO.ipynb -------------------------------------------------------------------------------- /examples/Example_3_Scatterplot_annotation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/examples/Example_3_Scatterplot_annotation.ipynb -------------------------------------------------------------------------------- /extras/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/extras/requirements.txt -------------------------------------------------------------------------------- /safepy/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /safepy/run.py: -------------------------------------------------------------------------------- 1 | ## command line -------------------------------------------------------------------------------- /safepy/safe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/safe.py -------------------------------------------------------------------------------- /safepy/safe_colormaps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/safe_colormaps.py -------------------------------------------------------------------------------- /safepy/safe_default.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/safe_default.ini -------------------------------------------------------------------------------- /safepy/safe_extras.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/safe_extras.py -------------------------------------------------------------------------------- /safepy/safe_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/safe_io.py -------------------------------------------------------------------------------- /safepy/utils/make_go.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/safepy/utils/make_go.py -------------------------------------------------------------------------------- /tests/test_enrichments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/tests/test_enrichments.py -------------------------------------------------------------------------------- /tests/test_imports.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/tests/test_imports.py -------------------------------------------------------------------------------- /tests/test_neighborhoods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/baryshnikova-lab/safepy/HEAD/tests/test_neighborhoods.py --------------------------------------------------------------------------------