├── LICENSE ├── README.md ├── environment.yml ├── graphics ├── overview.PNG └── overview.png └── src ├── Ecoli_Promoter_classification ├── Dataset.py ├── Functions.py ├── Logger.py ├── LrScheduler.py ├── Metrics.py ├── Network.py ├── evaluate.py ├── evaluate.sh ├── extract_motif.py ├── readme.md ├── run.sh ├── train.py └── v9d3.csv ├── Enchancer_classification ├── Dataset.py ├── Functions.py ├── Logger.py ├── LrScheduler.py ├── Metrics.py ├── Network.py ├── bert_enhancer_dataset.csv ├── evaluate.py ├── evaluate.sh ├── job.sh ├── job_eval.sh ├── run.sh ├── test.py ├── test.sh └── train.py ├── Eukaryotic_Promoters_Classification ├── README.md ├── human_non_tata │ ├── Dataset.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── human_non_tata_deepromoter │ ├── Dataset.py │ ├── DeePromoter.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── human_tata │ ├── Dataset.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── human_tata_deepromoter │ ├── Dataset.py │ ├── DeePromoter.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── mouse_non_tata │ ├── Dataset.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── mouse_non_tata_deepromoter │ ├── Dataset.py │ ├── DeePromoter.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── mouse_tata │ ├── Dataset.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── mouse_tata_deepromoter │ ├── Dataset.py │ ├── DeePromoter.py │ ├── Functions.py │ ├── Logger.py │ ├── LrScheduler.py │ ├── Metrics.py │ ├── Network.py │ ├── check_log.py │ ├── evaluate.py │ ├── extract_motif.py │ ├── run.sh │ └── train.py ├── run_human.sh └── run_mouse.sh ├── Non_Coding_Variant_Effects ├── Dataset.py ├── Functions.py ├── Logger.py ├── LrScheduler.py ├── Metrics.py ├── Network.py ├── compute_median_aucs.py ├── compute_val_aucs.py ├── preprocess_data.py ├── readme.md ├── restart.py ├── restart.sh ├── run.sh ├── test.py ├── test.sh └── train.py └── Viral_identification ├── Dataset.py ├── Functions.py ├── Logger.py ├── LrScheduler.py ├── Metrics.py ├── Network.py ├── evaluate_test.py ├── readme.md ├── run.sh ├── 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