├── .gitignore ├── .gitmodules ├── README.md ├── code ├── 0_Generate_invivo_dataset.ipynb ├── 0_Generate_synthetic_dataset.ipynb ├── 1_train_invivo.py ├── 1_train_synthetic.py ├── 2_tomtom_invivo.sh ├── 2_tomtom_synthetic.sh ├── 3_match_statistics_invivo.py ├── 3_match_statistics_synthetic.py ├── 4_2ndlayer_filter_analysis_invivo.py ├── 4_2ndlayer_filter_analysis_synthetic.py ├── 5_2ndlayer_tomtom_invivo.sh ├── 5_2ndlayer_tomtom_synthetic.sh ├── 6_2ndlayer_match_statistics_invivo.py ├── 6_2ndlayer_match_statistics_synthetic.py ├── __init__.py ├── deepomics │ ├── README.md │ ├── __init__.py │ ├── chars │ │ ├── A.eps │ │ ├── C.eps │ │ ├── E.eps │ │ ├── G.eps │ │ ├── H.eps │ │ ├── I.eps │ │ ├── L.eps │ │ ├── M.eps │ │ ├── P.eps │ │ ├── T.eps │ │ └── U.eps │ ├── explore.py │ ├── fit.py │ ├── init.py │ ├── layers │ │ ├── __init__.py │ │ ├── base.py │ │ ├── conv.py │ │ ├── dense.py │ │ ├── embedding.py │ │ ├── function.py │ │ ├── noise.py │ │ ├── norm.py │ │ ├── pool.py │ │ └── shape.py │ ├── metrics.py │ ├── neuralbuild.py │ ├── neuralbuild_scope.py │ ├── neuralnetwork.py │ ├── objectives.py │ ├── optimize.py │ ├── saliency.py │ ├── utils.py │ └── visualize.py ├── helper.py ├── models │ ├── __init__.py │ ├── cnn3_2.py │ ├── cnn3_50.py │ ├── cnn9_25.py │ ├── cnn9_4.py │ ├── cnn_1.py │ ├── cnn_10.py │ ├── cnn_100.py │ ├── cnn_1_3.py │ ├── cnn_2.py │ ├── cnn_25.py │ ├── cnn_25_120.py │ ├── cnn_25_60.py │ ├── cnn_25_90.py │ ├── cnn_2_1.py │ ├── cnn_4.py │ ├── cnn_50.py │ └── cnn_50_2.py └── run.sh └── data ├── JASPAR_CORE_2016_vertebrates.meme └── pfm_vertebrates.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/p-koo/learning_sequence_motifs/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | 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