├── .binder ├── postBuild ├── requirements.txt └── runtime.txt ├── .coveragerc ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── pr_validation.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── datasets ├── README.md └── synthetic │ ├── test_counts.csv │ └── test_metadata.csv ├── docs ├── Makefile ├── README.md ├── make.bat └── source │ ├── .DS_Store │ ├── _static │ ├── .DS_Store │ ├── download.svg │ ├── favicon.ico │ ├── fonts.css │ ├── logo.svg │ ├── owkin.css │ ├── pydeseq2_logo.png │ ├── pydeseq2_logo.svg │ ├── pydeseq2_logo_green.png │ └── sidebar.css │ ├── api │ ├── docstrings │ │ ├── pydeseq2.dds.DeseqDataSet.rst │ │ ├── pydeseq2.default_inference.DefaultInference.rst │ │ ├── pydeseq2.ds.DeseqStats.rst │ │ ├── pydeseq2.grid_search.rst │ │ ├── pydeseq2.inference.Inference.rst │ │ ├── pydeseq2.preprocessing.rst │ │ └── pydeseq2.utils.rst │ └── index.rst │ ├── conf.py │ ├── index.rst │ ├── refs.bib │ └── usage │ ├── contributing.rst │ ├── installation.rst │ ├── references.rst │ └── requirements.rst ├── examples ├── README.rst ├── plot_minimal_pydeseq2_pipeline.py ├── plot_pandas_io_example.py └── plot_step_by_step.py ├── pydeseq2 ├── __init__.py ├── __version__.py ├── dds.py ├── default_inference.py ├── ds.py ├── grid_search.py ├── inference.py ├── preprocessing.py └── utils.py ├── pyproject.toml └── tests ├── __init__.py ├── data ├── README.md ├── continuous │ ├── r_test_dispersions.csv │ ├── r_test_lfc_shrink_res.csv │ ├── r_test_res.csv │ ├── r_test_res_outliers.csv │ ├── r_test_size_factors.csv │ ├── test_counts.csv │ └── test_metadata.csv ├── large_counts │ ├── r_test_dispersions.csv │ ├── r_test_lfc_shrink_res.csv │ ├── r_test_res.csv │ └── r_test_size_factors.csv ├── multi_factor │ ├── r_test_dispersions.csv │ ├── r_test_lfc_shrink_res.csv │ ├── r_test_res.csv │ ├── r_test_res_outliers.csv │ └── r_test_size_factors.csv ├── single_factor │ ├── r_iterative_size_factors.csv │ ├── r_mean_vst.csv │ ├── r_test_dispersions.csv │ ├── r_test_lfc_shrink_no_apeAdapt_res.csv │ ├── r_test_lfc_shrink_res.csv │ ├── r_test_res.csv │ ├── r_test_res_greater.csv │ ├── r_test_res_greaterAbs.csv │ ├── r_test_res_less.csv │ ├── r_test_res_lessAbs.csv │ ├── r_test_res_mean_curve.csv │ ├── r_test_res_no_independent_filtering.csv │ ├── r_test_size_factors.csv │ ├── r_test_size_factors_poscount.csv │ ├── r_vst.csv │ └── r_vst_with_design.csv └── wide │ ├── r_test_dispersions.csv │ ├── r_test_res.csv │ ├── r_test_size_factors.csv │ ├── test_counts.csv │ └── test_metadata.csv ├── test_edge_cases.py ├── test_pydeseq2.py └── test_utils.py /.binder/postBuild: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/owkin/PyDESeq2/HEAD/.binder/postBuild 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