├── .codecov.yaml ├── .cruft.json ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml └── workflows │ ├── build.yaml │ ├── pydocstyle.yaml │ ├── release.yaml │ ├── ruff.yaml │ └── test.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── biome.jsonc ├── docs ├── Makefile ├── _static │ ├── .gitkeep │ ├── css │ │ └── custom.css │ └── img │ │ ├── crested_banner.png │ │ ├── crested_logo.png │ │ └── examples │ │ ├── bar_normalization_weights.png │ │ ├── bar_region.png │ │ ├── bar_region_predictions.png │ │ ├── contribution_scores.png │ │ ├── genomic_contributions.png │ │ ├── heatmap_correlations_predictions.png │ │ ├── heatmap_self_correlations.png │ │ ├── hist_distribution.png │ │ ├── locus_locus_scoring.png │ │ ├── locus_track.png │ │ ├── pattern_class_instances.png │ │ ├── pattern_clustermap.png │ │ ├── pattern_selected_instances.png │ │ ├── pattern_similarity_heatmap.png │ │ ├── pattern_tf_motif_clustermap.png │ │ ├── scatter_class_density.png │ │ └── violin_correlations.png ├── _templates │ ├── .gitkeep │ └── autosummary │ │ └── class.rst ├── api │ ├── datasets.md │ ├── index.md │ ├── io.md │ ├── plotting │ │ ├── bar.md │ │ ├── heatmap.md │ │ ├── hist.md │ │ ├── index.md │ │ ├── locus.md │ │ ├── patterns.md │ │ ├── scatter.md │ │ └── violin.md │ ├── preprocessing.md │ ├── tools │ │ ├── data.md │ │ ├── index.md │ │ ├── losses.md │ │ ├── metrics.md │ │ ├── modisco.md │ │ └── zoo.md │ └── utils.md ├── changelog.md ├── conf.py ├── contributing.md ├── extensions │ └── typed_returns.py ├── howtocite.md ├── index.md ├── installation.md ├── license.md ├── models │ ├── BICCN │ │ ├── borzoi_biccn.rst │ │ ├── deepbiccn.rst │ │ ├── deepbiccn2.rst │ │ ├── index.md │ │ └── mousecortex_hydrop.rst │ ├── Brain │ │ ├── deepchickenbrain1.rst │ │ ├── deepchickenbrain2.rst │ │ ├── deephumanbrain.rst │ │ ├── deephumancortex1.rst │ │ ├── deephumancortex2.rst │ │ ├── deepmousebrain1.rst │ │ ├── deepmousebrain2.rst │ │ ├── deepmousebrain3.rst │ │ └── index.md │ ├── Cancer │ │ ├── deepccl.rst │ │ ├── deepglioma.rst │ │ ├── deepmel1.rst │ │ ├── deepmel2.rst │ │ ├── deepmel2_gabpa.rst │ │ └── index.md │ ├── EnformerBorzoi │ │ ├── borzoi.rst │ │ ├── enformer.rst │ │ └── index.md │ ├── Fly │ │ ├── deepflybrain.rst │ │ ├── embryo_10x.rst │ │ ├── embryo_hydrop.rst │ │ └── index.md │ ├── Liver │ │ ├── deepliver accessibility.rst │ │ ├── deepliver activity.rst │ │ ├── deepliver zonation.rst │ │ └── index.md │ ├── deeppbmc.rst │ ├── deepzebrafish.rst │ └── index.md ├── references.bib ├── references.md └── tutorials │ ├── borzoi_atac_finetuning.ipynb │ ├── custom_models.ipynb │ ├── data │ └── .gitignore │ ├── enhancer_code_analysis.ipynb │ ├── index.md │ ├── model_database_example.ipynb │ ├── model_training_and_eval.ipynb │ ├── multi_gpu.ipynb │ └── topic_classification.ipynb ├── pyproject.toml ├── scripts └── model_porting │ ├── borzoi_to_crested.py │ └── enf_to_crested.py ├── src └── crested │ ├── __init__.py │ ├── _backend.py │ ├── _conf.py │ ├── _datasets.py │ ├── _genome.py │ ├── _io.py │ ├── pl │ ├── __init__.py │ ├── _utils.py │ ├── bar │ │ ├── __init__.py │ │ ├── _normalization_weights.py │ │ └── _region.py │ ├── heatmap │ │ ├── __init__.py │ │ └── _correlations.py │ ├── hist │ │ ├── __init__.py │ │ └── _distribution.py │ ├── locus │ │ ├── __init__.py │ │ ├── _locus_scoring.py │ │ └── _track.py │ ├── patterns │ │ ├── __init__.py │ │ ├── _contribution_scores.py │ │ ├── _enhancer_design.py │ │ ├── _modisco_results.py │ │ └── _utils.py │ ├── scatter │ │ ├── __init__.py │ │ └── _class_density.py │ └── violin │ │ ├── __init__.py │ │ └── _correlations.py │ ├── pp │ ├── __init__.py │ ├── _filter.py │ ├── _normalization.py │ ├── _regions.py │ ├── _split.py │ └── _utils.py │ ├── tl │ ├── __init__.py │ ├── _configs.py │ ├── _crested.py │ ├── _explainer.py │ ├── _explainer_tf.py │ ├── _explainer_torch.py │ ├── _tools.py │ ├── _utils.py │ ├── data │ │ ├── __init__.py │ │ ├── _anndatamodule.py │ │ ├── _dataloader.py │ │ └── _dataset.py │ ├── losses │ │ ├── __init__.py │ │ ├── _cosinemse.py │ │ ├── _cosinemse_log.py │ │ ├── _poisson.py │ │ └── _poissonmultinomial.py │ ├── metrics │ │ ├── __init__.py │ │ ├── _concordancecorr.py │ │ ├── _pearsoncorr.py │ │ ├── _pearsoncorrlog.py │ │ ├── _spearmancorr.py │ │ └── _zeropenalty.py │ ├── modisco │ │ ├── __init__.py │ │ ├── _modisco_utils.py │ │ └── _tfmodisco.py │ └── zoo │ │ ├── __init__.py │ │ ├── _basenji.py │ │ ├── _borzoi.py │ │ ├── _deeptopic_cnn.py │ │ ├── _deeptopic_lstm.py │ │ ├── _dilated_cnn.py │ │ ├── _dilated_cnn_decoupled.py │ │ ├── _enformer.py │ │ ├── _simple_convnet.py │ │ └── utils │ │ ├── __init__.py │ │ ├── _attention.py │ │ └── _layers.py │ └── utils │ ├── __init__.py │ ├── _logging.py │ ├── _model_utils.py │ ├── _seq_utils.py │ └── _utils.py └── tests ├── __init__.py ├── _utils.py ├── conftest.py ├── data ├── test.chrom.sizes ├── test.regions.bed ├── 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