README.md
pyproject.toml
setup.py
src/embkit/__init__.py
src/embkit/__main__.py
src/embkit/align.py
src/embkit/bmeg.py
src/embkit/pathway.py
src/embkit/version.py
src/embkit.egg-info/PKG-INFO
src/embkit.egg-info/SOURCES.txt
src/embkit.egg-info/dependency_links.txt
src/embkit.egg-info/entry_points.txt
src/embkit.egg-info/requires.txt
src/embkit.egg-info/top_level.txt
src/embkit/c_bio/__init__.py
src/embkit/c_bio/api.py
src/embkit/commands/__init__.py
src/embkit/commands/align.py
src/embkit/commands/cbio.py
src/embkit/commands/matrix.py
src/embkit/commands/model.py
src/embkit/commands/protein.py
src/embkit/commands/resources.py
src/embkit/constraints/__init__.py
src/embkit/constraints/pathway_constraint.py
src/embkit/datasets/__init__.py
src/embkit/encoding/__init__.py
src/embkit/encoding/genome.py
src/embkit/encoding/protein.py
src/embkit/estimator/__init__.py
src/embkit/estimator/vae_estimator.py
src/embkit/factory/__init__.py
src/embkit/factory/core.py
src/embkit/factory/layers.py
src/embkit/factory/mapping.py
src/embkit/factory/registry.py
src/embkit/files/__init__.py
src/embkit/files/h5.py
src/embkit/files/json.py
src/embkit/files/loaders.py
src/embkit/files/read_csv.py
src/embkit/losses/__init__.py
src/embkit/losses/vae_loss.py
src/embkit/metrics/__init__.py
src/embkit/metrics/distance/__init__.py
src/embkit/metrics/distance/metrics.py
src/embkit/models/__init__.py
src/embkit/models/ffnn.py
src/embkit/models/vae/__init__.py
src/embkit/models/vae/base_vae.py
src/embkit/models/vae/decoder.py
src/embkit/models/vae/encoder.py
src/embkit/models/vae/net_vae.py
src/embkit/models/vae/rna_vae.py
src/embkit/models/vae/vae.py
src/embkit/modules/__init__.py
src/embkit/modules/masked_linear.py
src/embkit/modules/pairwise_comparison_layer.py
src/embkit/modules/tsp.py
src/embkit/optimize/__init__.py
src/embkit/preprocessing/__init__.py
src/embkit/preprocessing/dataset.py
src/embkit/preprocessing/normalize.py
src/embkit/resources/__init__.py
src/embkit/resources/c_bio_portal.py
src/embkit/resources/gtex.py
src/embkit/resources/hugo.py
src/embkit/resources/resource.py
src/embkit/resources/sif.py
src/embkit/resources/util.py
src/embkit/utilities/__init__.py
src/embkit/utilities/kmeans.py
src/embkit/utilities/pca.py
tests/test_main.py