LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
chrombpnet/CHROMBPNET.py
chrombpnet/__init__.py
chrombpnet/parsers.py
chrombpnet/pipelines.py
chrombpnet.egg-info/PKG-INFO
chrombpnet.egg-info/SOURCES.txt
chrombpnet.egg-info/dependency_links.txt
chrombpnet.egg-info/entry_points.txt
chrombpnet.egg-info/not-zip-safe
chrombpnet.egg-info/requires.txt
chrombpnet.egg-info/top_level.txt
chrombpnet/data/ATAC.ref.motifs.txt
chrombpnet/data/DNASE.ref.motifs.txt
chrombpnet/data/__init__.py
chrombpnet/data/motif_to_pwm.ATAC.tsv
chrombpnet/data/motif_to_pwm.DNASE.tsv
chrombpnet/data/motif_to_pwm.TF.tsv
chrombpnet/data/motifs.meme.txt
chrombpnet/evaluation/__init__.py
chrombpnet/evaluation/interpret/__init__.py
chrombpnet/evaluation/interpret/input_utils.py
chrombpnet/evaluation/interpret/interpret.py
chrombpnet/evaluation/interpret/shap_utils.py
chrombpnet/evaluation/invivo_footprints/__init__.py
chrombpnet/evaluation/invivo_footprints/run_tfmodisco.py
chrombpnet/evaluation/invivo_footprints/tf_modiscohits.py
chrombpnet/evaluation/make_bigwigs/__init__.py
chrombpnet/evaluation/make_bigwigs/bigwig_helper.py
chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py
chrombpnet/evaluation/make_bigwigs/predict_to_bigwig.py
chrombpnet/evaluation/marginal_footprints/__init__.py
chrombpnet/evaluation/marginal_footprints/marginal_footprinting.py
chrombpnet/evaluation/modisco/__init__.py
chrombpnet/evaluation/modisco/convert_html_to_pdf.py
chrombpnet/evaluation/modisco/fetch_tomtom.py
chrombpnet/evaluation/modisco/run_modisco.py
chrombpnet/evaluation/modisco/visualize_motif_matches.py
chrombpnet/evaluation/variant_effect_prediction/__init__.py
chrombpnet/evaluation/variant_effect_prediction/snp_generator.py
chrombpnet/evaluation/variant_effect_prediction/snp_scoring.py
chrombpnet/evaluation/variant_effect_prediction/testing.py
chrombpnet/helpers/__init__.py
chrombpnet/helpers/generate_reports/__init__.py
chrombpnet/helpers/generate_reports/make_html.py
chrombpnet/helpers/generate_reports/make_html_bias.py
chrombpnet/helpers/hyperparameters/__init__.py
chrombpnet/helpers/hyperparameters/find_bias_hyperparams.py
chrombpnet/helpers/hyperparameters/find_chrombpnet_hyperparams.py
chrombpnet/helpers/hyperparameters/param_utils.py
chrombpnet/helpers/make_chr_splits/__init__.py
chrombpnet/helpers/make_chr_splits/splits.py
chrombpnet/helpers/make_gc_matched_negatives/__init__.py
chrombpnet/helpers/make_gc_matched_negatives/get_gc_content.py
chrombpnet/helpers/make_gc_matched_negatives/get_gc_matched_negatives.py
chrombpnet/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets/__init__.py
chrombpnet/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets/get_genomewide_gc_bins.py
chrombpnet/helpers/preprocessing/__init__.py
chrombpnet/helpers/preprocessing/auto_shift_detect.py
chrombpnet/helpers/preprocessing/reads_to_bigwig.py
chrombpnet/helpers/preprocessing/analysis/__init__.py
chrombpnet/helpers/preprocessing/analysis/build_pwm_from_bigwig.py
chrombpnet/training/__init__.py
chrombpnet/training/metrics.py
chrombpnet/training/predict.py
chrombpnet/training/train.py
chrombpnet/training/data_generators/__init__.py
chrombpnet/training/data_generators/batchgen_generator.py
chrombpnet/training/data_generators/initializers.py
chrombpnet/training/models/__init__.py
chrombpnet/training/models/bpnet_model.py
chrombpnet/training/models/chrombpnet_with_bias_model.py
chrombpnet/training/utils/__init__.py
chrombpnet/training/utils/argmanager.py
chrombpnet/training/utils/augment.py
chrombpnet/training/utils/callbacks.py
chrombpnet/training/utils/data_utils.py
chrombpnet/training/utils/losses.py
chrombpnet/training/utils/metrics_utils.py
chrombpnet/training/utils/one_hot.py
tests/full_workflow.sh
tests/genomewide_gc_bin_test.sh
tests/test_pred_to_bigwig.sh
workflows/train_bias_model.sh
workflows/train_chrombpnet_model.sh