├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── deepDegron ├── __init__.py ├── deep_degron.py ├── degron_pred.py ├── motif_analysis.py ├── pvalue.py ├── run_saturation_mutagenesis.py ├── score_mutations.py ├── sequence_context.py ├── simulation.py ├── statistical_test.py ├── train_cterm_nn.py ├── train_nterm_nn.py ├── utils.py └── variants.py ├── docs ├── GATA3_delta_degron_potential.txt ├── GATA3_result.txt ├── conf.py ├── download.rst ├── faq.rst ├── file_format.rst ├── images │ └── deepDegron_logo.png ├── index.rst ├── installation.rst └── tutorial.rst ├── environment.yml ├── models ├── cterm │ ├── neural_network_bag_of_amino_acids.pickle │ └── neural_network_pos_specific.pickle └── nterm │ ├── neural_network_bag_of_amino_acids.pickle │ └── neural_network_pos_specific.pickle ├── requirements.txt ├── setup.py ├── tests ├── data │ ├── CTNNB1_mutations_ucec.txt │ ├── MN1_example.txt │ ├── NFE2L2_mutations_lusc.txt │ ├── ctnnb1_phosphodegron_sites.txt │ ├── gata3_mutations.txt │ ├── gps_cterminal_degron_screen_500.txt │ └── nfe2l2_degron_sites.txt ├── test_cterm_train.py ├── test_ctnnb1_mutation.py ├── test_mn1_mutation.py ├── test_nfe2l2_mutation.py └── test_score.py └── train_data ├── gps_cterminal_degron_screen.txt └── gps_nterminal_degron_screen.txt /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/README.md -------------------------------------------------------------------------------- /deepDegron/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = '1.1.0' 2 | -------------------------------------------------------------------------------- /deepDegron/deep_degron.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/deep_degron.py -------------------------------------------------------------------------------- /deepDegron/degron_pred.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/degron_pred.py -------------------------------------------------------------------------------- /deepDegron/motif_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/motif_analysis.py -------------------------------------------------------------------------------- /deepDegron/pvalue.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/pvalue.py -------------------------------------------------------------------------------- /deepDegron/run_saturation_mutagenesis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/run_saturation_mutagenesis.py -------------------------------------------------------------------------------- /deepDegron/score_mutations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/score_mutations.py -------------------------------------------------------------------------------- /deepDegron/sequence_context.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/sequence_context.py -------------------------------------------------------------------------------- /deepDegron/simulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/simulation.py -------------------------------------------------------------------------------- /deepDegron/statistical_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/statistical_test.py -------------------------------------------------------------------------------- /deepDegron/train_cterm_nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/train_cterm_nn.py -------------------------------------------------------------------------------- /deepDegron/train_nterm_nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/train_nterm_nn.py -------------------------------------------------------------------------------- /deepDegron/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/utils.py -------------------------------------------------------------------------------- /deepDegron/variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/deepDegron/variants.py -------------------------------------------------------------------------------- /docs/GATA3_delta_degron_potential.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/GATA3_delta_degron_potential.txt -------------------------------------------------------------------------------- /docs/GATA3_result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/GATA3_result.txt -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/download.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/download.rst -------------------------------------------------------------------------------- /docs/faq.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/faq.rst -------------------------------------------------------------------------------- /docs/file_format.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/file_format.rst -------------------------------------------------------------------------------- /docs/images/deepDegron_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/images/deepDegron_logo.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/tutorial.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/docs/tutorial.rst -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/environment.yml -------------------------------------------------------------------------------- /models/cterm/neural_network_bag_of_amino_acids.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/models/cterm/neural_network_bag_of_amino_acids.pickle -------------------------------------------------------------------------------- /models/cterm/neural_network_pos_specific.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/models/cterm/neural_network_pos_specific.pickle -------------------------------------------------------------------------------- /models/nterm/neural_network_bag_of_amino_acids.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/models/nterm/neural_network_bag_of_amino_acids.pickle -------------------------------------------------------------------------------- /models/nterm/neural_network_pos_specific.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/models/nterm/neural_network_pos_specific.pickle -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/setup.py -------------------------------------------------------------------------------- /tests/data/CTNNB1_mutations_ucec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/CTNNB1_mutations_ucec.txt -------------------------------------------------------------------------------- /tests/data/MN1_example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/MN1_example.txt -------------------------------------------------------------------------------- /tests/data/NFE2L2_mutations_lusc.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/NFE2L2_mutations_lusc.txt -------------------------------------------------------------------------------- /tests/data/ctnnb1_phosphodegron_sites.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/ctnnb1_phosphodegron_sites.txt -------------------------------------------------------------------------------- /tests/data/gata3_mutations.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/gata3_mutations.txt -------------------------------------------------------------------------------- /tests/data/gps_cterminal_degron_screen_500.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/gps_cterminal_degron_screen_500.txt -------------------------------------------------------------------------------- /tests/data/nfe2l2_degron_sites.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/data/nfe2l2_degron_sites.txt -------------------------------------------------------------------------------- /tests/test_cterm_train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/test_cterm_train.py -------------------------------------------------------------------------------- /tests/test_ctnnb1_mutation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/test_ctnnb1_mutation.py -------------------------------------------------------------------------------- /tests/test_mn1_mutation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/test_mn1_mutation.py -------------------------------------------------------------------------------- /tests/test_nfe2l2_mutation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/test_nfe2l2_mutation.py -------------------------------------------------------------------------------- /tests/test_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/tests/test_score.py -------------------------------------------------------------------------------- /train_data/gps_cterminal_degron_screen.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/train_data/gps_cterminal_degron_screen.txt -------------------------------------------------------------------------------- /train_data/gps_nterminal_degron_screen.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctokheim/deepDegron/HEAD/train_data/gps_nterminal_degron_screen.txt --------------------------------------------------------------------------------