├── .coverage ├── .github ├── pull_request_template.md └── workflows │ └── CI.yml ├── .pre-commit-config.yaml ├── Dockerfile ├── LICENSE ├── README.md ├── codecov.yml ├── diffexpr ├── __init__.py ├── py_deseq.py └── py_pathway.py ├── environment.yml ├── example ├── deseq_example.ipynb └── jupyter.png ├── poetry.lock ├── pyproject.toml ├── requirements.txt ├── setup.R ├── setup.py └── test ├── data ├── ercc.tsv ├── quant1 │ └── abundance.h5 └── quant2 │ └── abundance.h5 ├── deseq.R ├── test_deseq.py └── test_pathways.py /.coverage: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/.coverage -------------------------------------------------------------------------------- /.github/pull_request_template.md: -------------------------------------------------------------------------------- 1 | Description of what this PR does 2 | 3 | ## Checklist 4 | - [ ] CI pass? 5 | -------------------------------------------------------------------------------- /.github/workflows/CI.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/.github/workflows/CI.yml -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/README.md -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/codecov.yml -------------------------------------------------------------------------------- /diffexpr/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /diffexpr/py_deseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/diffexpr/py_deseq.py -------------------------------------------------------------------------------- /diffexpr/py_pathway.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/diffexpr/py_pathway.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/environment.yml -------------------------------------------------------------------------------- /example/deseq_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/example/deseq_example.ipynb -------------------------------------------------------------------------------- /example/jupyter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/example/jupyter.png -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/poetry.lock -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/setup.R -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/setup.py -------------------------------------------------------------------------------- /test/data/ercc.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/data/ercc.tsv -------------------------------------------------------------------------------- /test/data/quant1/abundance.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/data/quant1/abundance.h5 -------------------------------------------------------------------------------- /test/data/quant2/abundance.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/data/quant2/abundance.h5 -------------------------------------------------------------------------------- /test/deseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/deseq.R -------------------------------------------------------------------------------- /test/test_deseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/test_deseq.py -------------------------------------------------------------------------------- /test/test_pathways.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wckdouglas/diffexpr/HEAD/test/test_pathways.py --------------------------------------------------------------------------------