CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README-pypi.md
README.md
pyproject.toml
checks/test_workflow.py
docs/data.md
docs/models.md
docs/releasing.md
docs/reviewing.md
docs/submitting.md
docs/tasks.md
docs/assets/capabilities-narrow-dark.svg
docs/assets/capabilities-narrow-light.svg
docs/assets/capabilities-wide-dark.svg
docs/assets/capabilities-wide-light.svg
docs/assets/readme-banner.png
docs/assets/results-dark.svg
docs/assets/results-light.svg
src/bend2/__init__.py
src/bend2/__main__.py
src/bend2/_combine.py
src/bend2/_linear.py
src/bend2/assets.json
src/bend2/cache.py
src/bend2/catalog.py
src/bend2/cli.py
src/bend2/datasets.py
src/bend2/github.py
src/bend2/huggingface.py
src/bend2/model.py
src/bend2/planning.py
src/bend2/readouts.py
src/bend2/reference_models.py
src/bend2/results.py
src/bend2/reviews.py
src/bend2/runner.py
src/bend2/submissions.py
src/bend2.egg-info/PKG-INFO
src/bend2.egg-info/SOURCES.txt
src/bend2.egg-info/dependency_links.txt
src/bend2.egg-info/entry_points.txt
src/bend2.egg-info/requires.txt
src/bend2.egg-info/top_level.txt
src/bend2/_data/atlas-candidate-activities.parquet
src/bend2/_data/atlas-population.parquet
src/bend2/_data/atlas-programs.csv
src/bend2/_data/atlas-source-activities.parquet
src/bend2/_data/gtex-genes.tsv
src/bend2/_data/gtex-targets.npz
src/bend2/_data/prior-panel.parquet
src/bend2/_data/prior-query-seeds.json
src/bend2/_data/siraj-numeric-reference.npz
src/bend2/_data/siraj_selective.parquet
src/bend2/_examples/custom.py
src/bend2/_examples/dnabert2.py
src/bend2/_examples/huggingface.py
src/bend2/_examples/ntv3_prior.py
src/bend2/_rescoring/__init__.py
src/bend2/_rescoring/interventions.py
src/bend2/_rescoring/panels.py
src/bend2/_tasks/__init__.py
src/bend2/_tasks/_siraj.py
src/bend2/_tasks/atlas_profile.py
src/bend2/_tasks/background.py
src/bend2/_tasks/cell_selective.py
src/bend2/_tasks/context.py
src/bend2/_tasks/opensplice.py
src/bend2/_tasks/prior.py
src/bend2/_tasks/repair_percentile.py
src/bend2/_tasks/tissue_identification.py