Enhancer design manuscript data and models

This repository holds the trained DNA accessibility and enhancer activity models, and the data used to train and evaluate the model.

Files for DNA accessibility models:

Accessibility_models_training_data.tar.gz

_sequences_.fa

FASTA files with DNA sequences of genomic regions from train/val/test sets.

_sequences_activity_.txt

Files with accessibility scores for sequences from train/val/test sets.

Accessibility_model_files.tar.gz

model.h5 and model.json files for each Results___DeepSTARR2_

Accessibility_models_test_set_predictions.rds

RDS object with predictions for accessibility

Files for enhancer activity models:

EnhancerActivity_model_files.tar.gz

_sequences_.fa

FASTA files with DNA sequences of genomic regions from train/val/test sets.

_sequences_activity_.txt

Files with enhancer activity labels for sequences from train/val/test sets.

EnhancerActivity_model_files.tar.gz

model.h5, model.json and Model_evaluation.pdf files for each Results___

EnhancerActivity_models_clean_evaluation_data.rds

RDS object with sequences used for final evaluation of the models

EnhancerActivity_models_results_per_tissue_test_set.rds

RDS object with predictions and results of the enhancer activity models