├── .gitignore ├── DIGDriver ├── __init__.py ├── auxilaries │ ├── __init__.py │ ├── concat_data.py │ ├── unzip_h5.py │ └── utils.py ├── data │ ├── dndscv_gene_cds.bed.gz │ ├── genes.MARTINCORENA.bed │ ├── genes_CGC_ALL.txt │ ├── genes_CGC_ALL.txt.bck │ ├── genes_CGC_ONC.txt │ ├── genes_CGC_TSG.txt │ ├── genes_MSK_230.txt │ ├── genes_MSK_341.txt │ ├── genes_MSK_410.txt │ ├── genes_MSK_468.txt │ ├── genes_metabric_173.txt │ ├── genes_ucla_1202.txt │ └── refcds_hg19.rda ├── data_tools │ ├── DIG_auto.py │ ├── __init__.py │ ├── auto_runner.py │ ├── mappability_tools.py │ ├── mutation_tools.py │ └── track_selector.py ├── driver_model │ ├── __init__.py │ ├── onthefly_tools.py │ └── transfer_tools.py ├── region_model │ ├── .DS_Store │ ├── __init__.py │ ├── autoencoders │ │ ├── AE_vec_predictors.py │ │ ├── ae_nets │ │ │ ├── CNNs.py │ │ │ └── fc_nets.py │ │ └── autoencoder_main.py │ ├── data_aux │ │ ├── dataset_generator.py │ │ └── mut_dataset.py │ ├── feature_vectors │ │ ├── gaussian_process.py │ │ ├── get_feature_vectors.py │ │ └── get_heldout_feature_vectors.py │ ├── kfold_mutations_main.py │ ├── mutations_main.py │ ├── nets │ │ ├── __init__.py │ │ ├── cnn_predictors.py │ │ ├── densenet.py │ │ ├── resnet.py │ │ └── rnn_predictors.py │ ├── perturbations_confidance │ │ ├── __init__.py │ │ ├── confidance_perturbations_estimate.py │ │ ├── configs │ │ │ ├── __init__.py │ │ │ ├── config_confidance.json │ │ │ └── config_confidance_kfold.json │ │ └── kfold_test_model_confidance.py │ ├── region_model_tools.py │ ├── train_nn.sh │ └── trainers │ │ ├── __init__.py │ │ ├── gp_trainer.py │ │ └── nn_trainer.py └── sequence_model │ ├── __init__.py │ ├── genic_driver_tools.py │ ├── gp_tools.py │ ├── nb_model.py │ └── sequence_tools.py ├── LICENSE ├── README.md ├── __init__.py ├── conda-recipe └── meta.yaml ├── examples ├── README.md ├── gene_driver.sh ├── mutation_driver.sh └── noncoding_driver.sh ├── requirements.txt ├── scripts ├── DataExtractor.py ├── DigDriver.py ├── DigPreprocess.py ├── DigPretrain.py ├── filter_hypermut.py └── mutationFunction.R └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/maxwellsh/DIGDriver/HEAD/.gitignore -------------------------------------------------------------------------------- /DIGDriver/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/maxwellsh/DIGDriver/HEAD/DIGDriver/__init__.py -------------------------------------------------------------------------------- /DIGDriver/auxilaries/__init__.py: -------------------------------------------------------------------------------- 1 | ## python init file 2 | -------------------------------------------------------------------------------- /DIGDriver/auxilaries/concat_data.py: -------------------------------------------------------------------------------- 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