├── .gitignore ├── LICENSE ├── README.md ├── covadapt ├── __init__.py ├── eigvals_lw.py ├── eigvals_reg.py ├── matrix.py ├── potential.py └── spd_manifold.py ├── examples ├── bayes-deseq2.ipynb ├── metric-selection-criterion.ipynb ├── pasilla_gene_counts.tsv └── test_train_split.ipynb ├── notebooks └── covadapt_intro.ipynb ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.egg-info 2 | __pycache__ 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/README.md -------------------------------------------------------------------------------- /covadapt/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/__init__.py -------------------------------------------------------------------------------- /covadapt/eigvals_lw.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/eigvals_lw.py -------------------------------------------------------------------------------- /covadapt/eigvals_reg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/eigvals_reg.py -------------------------------------------------------------------------------- /covadapt/matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/matrix.py -------------------------------------------------------------------------------- /covadapt/potential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/potential.py -------------------------------------------------------------------------------- /covadapt/spd_manifold.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/covadapt/spd_manifold.py -------------------------------------------------------------------------------- /examples/bayes-deseq2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/examples/bayes-deseq2.ipynb -------------------------------------------------------------------------------- /examples/metric-selection-criterion.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/examples/metric-selection-criterion.ipynb -------------------------------------------------------------------------------- /examples/pasilla_gene_counts.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/examples/pasilla_gene_counts.tsv -------------------------------------------------------------------------------- /examples/test_train_split.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/examples/test_train_split.ipynb -------------------------------------------------------------------------------- /notebooks/covadapt_intro.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/notebooks/covadapt_intro.ipynb -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aseyboldt/covadapt/HEAD/setup.py --------------------------------------------------------------------------------