.readthedocs.yml
LICENSE.md
MANIFEST.in
README.md
pyproject.toml
docs/images/deeprm.png
docs/images/deeprm_architecture.png
docs/images/deeprm_inference_pipeline.png
docs/images/deeprm_train_pipeline.png
docs/source/advanced-installation.md
docs/source/conf.py
docs/source/index.md
docs/source/installation.md
docs/source/license.md
docs/source/quickstart.md
docs/source/troubleshooting.md
docs/source/usage.md
docs/source/_static/.gitkeep
docs/source/_templates/.gitkeep
docs/source/api/index.md
docs/source/api/inference.md
docs/source/api/model.md
docs/source/api/qc.md
docs/source/api/train.md
docs/source/api/utils.md
docs/source/cli/call.md
docs/source/cli/check.md
docs/source/cli/index.md
docs/source/cli/qc.md
docs/source/cli/train.md
src/deeprm/__init__.py
src/deeprm/__main__.py
src/deeprm/cli.py
src/deeprm/inference/__init__.py
src/deeprm/inference/cli.py
src/deeprm/inference/deeprm_preprocess
src/deeprm/inference/inference.py
src/deeprm/inference/inference_dataloader.py
src/deeprm/inference/inference_preprocess.py
src/deeprm/inference/inference_preprocess_python.py
src/deeprm/inference/pileup_deeprm.py
src/deeprm/inference/pileup_genomic.py
src/deeprm/model/__init__.py
src/deeprm/model/deeprm_model.py
src/deeprm/qc/__init__.py
src/deeprm/qc/cli.py
src/deeprm/qc/inspect_alignment.py
src/deeprm/qc/inspect_block.py
src/deeprm/qc/inspect_run.py
src/deeprm/train/__init__.py
src/deeprm/train/cli.py
src/deeprm/train/extract_block.py
src/deeprm/train/train.py
src/deeprm/train/train_compile.py
src/deeprm/train/train_dataloader.py
src/deeprm/train/train_preprocess.py
src/deeprm/train/config/dag_config.json
src/deeprm/utils/__init__.py
src/deeprm/utils/activations.py
src/deeprm/utils/check_deps.py
src/deeprm/utils/check_installation.py
src/deeprm/utils/logging.py
src/deeprm/utils/memory.py
src/deeprm/utils/utils.py
src/deeprm/weight/deeprm_weights.pt
tests/test_cli_help.py
tests/test_imports.py