├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── bend ├── __init__.py ├── io │ ├── __init__.py │ └── sequtils.py ├── models │ ├── __init__.py │ ├── awd_lstm.py │ ├── basset.py │ ├── dilated_cnn.py │ ├── dnabert2.py │ ├── dnabert2_padding.py │ ├── downstream.py │ ├── gena_lm.py │ └── hyena_dna.py └── utils │ ├── __init__.py │ ├── data_downstream.py │ ├── download.py │ ├── embedders.py │ ├── retrieve_from_bed.py │ ├── sequences.py │ └── task_trainer.py ├── conf ├── config.yaml ├── datadims │ ├── dimensions │ │ └── datadims.yaml │ ├── downstream_downsample.yaml │ ├── embedding_dims.yaml │ ├── label_dims.yaml │ └── seq_lengths.yaml ├── embedding │ └── embed.yaml ├── hydra │ └── multirun.yaml ├── supervised_encoder │ ├── basset-supervised.yaml │ └── resnet-supervised.yaml └── supervised_tasks │ ├── chromatin_accessibility.yaml │ ├── cpg_methylation.yaml │ ├── enhancer_annotation.yaml │ ├── gene_finding.yaml │ └── histone_modification.yaml ├── docs ├── Makefile ├── make.bat ├── modules.rst ├── requirements.txt └── source │ ├── adding_embedders.rst │ ├── bend.io.rst │ ├── bend.models.rst │ ├── bend.rst │ ├── bend.utils.embedders.rst │ ├── bend.utils.rst │ ├── conf.py │ ├── hydra.rst │ ├── index.rst │ └── modules.rst ├── examples ├── Basset │ ├── notebook.ipynb │ └── samples.bed ├── meta │ ├── chr19.fa │ └── chr19.fa.fai └── unsupervised_variant_effects.ipynb ├── pyproject.toml ├── readthedocs.yaml ├── requirements.txt ├── scripts ├── download_bend.py ├── list_metrics.py ├── precompute_embeddings.py ├── predict_variant_effects.py ├── run_variant_effects.sh └── train_on_task.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/frederikkemarin/BEND/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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