.gitignore
LICENSE
README.md
config.yaml
pyproject.toml
uv.lock
.github/workflows/publish.yml
.github/workflows/tests.yml
sample_data/protrider_sample_dataset.tsv
sample_data/sample_annotations.tsv
src/protrider/__init__.py
src/protrider/cli.py
src/protrider/config.py
src/protrider/pipeline.py
src/protrider/plots.py
src/protrider/stats.py
src/protrider.egg-info/PKG-INFO
src/protrider.egg-info/SOURCES.txt
src/protrider.egg-info/dependency_links.txt
src/protrider.egg-info/entry_points.txt
src/protrider.egg-info/requires.txt
src/protrider.egg-info/top_level.txt
src/protrider/datasets/__init__.py
src/protrider/datasets/covariates.py
src/protrider/datasets/datasets.py
src/protrider/datasets/protein_intensities.py
src/protrider/model/__init__.py
src/protrider/model/model.py
src/protrider/model/model_helper.py
tests/README.md
tests/__init__.py
tests/conftest.py
tests/test_config.py
tests/test_covariates.py
tests/test_dataset.py
tests/test_model_save_load.py
tests/test_pipeline_config.py
tests/test_pipeline_features.py
tests/test_pipeline_misc.py
tests/test_pipeline_standard.py