.gitignore
LICENSE
MANIFEST.in
history.md
readme.md
requirements.txt
setup.py
.github/pull_request_template.md
.github/ISSUE_TEMPLATE/config.yml
HAllA.egg-info/PKG-INFO
HAllA.egg-info/SOURCES.txt
HAllA.egg-info/dependency_links.txt
HAllA.egg-info/entry_points.txt
HAllA.egg-info/requires.txt
HAllA.egg-info/top_level.txt
examples/PRISM/X_dataset.txt
examples/PRISM/Y_dataset.txt
examples/PRISM/run.sh
examples/PRISM/standards.txt
examples/nutrimouse/gene.txt
examples/nutrimouse/lipid.txt
examples/nutrimouse/run.sh
halla/__init__.py
halla/config.yaml
halla/config_loader.py
halla/hierarchy.py
halla/logger.py
halla/main.py
halla/utils/__init__.py
halla/utils/data.py
halla/utils/filesystem.py
halla/utils/report.py
halla/utils/similarity.py
halla/utils/stats.py
halla/utils/tree.py
scripts/__init__.py
scripts/diagnostic_plot.py
scripts/halla.py
scripts/hallagram.py
scripts/loader.py
scripts/synthetic_data.py
tests/run_tests.py
tests/test_utils_data.py
tests/test_utils_stats.py
tests/test_utils_tree.py
tests/utils.py