├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── Pipfile ├── Pipfile.lock ├── README.rst ├── _readme.md ├── astir ├── __init__.py ├── astir.py ├── data │ ├── __init__.py │ ├── data_readers.py │ ├── rds_reader.R │ ├── scdataset.py │ └── test_rds.csv └── models │ ├── __init__.py │ ├── abstract.py │ ├── cellstate.py │ ├── cellstate_recognet.py │ ├── celltype.py │ └── celltype_recognet.py ├── bin └── astir ├── docs ├── Makefile ├── astir.data.rst ├── astir.models.rst ├── astir.rst ├── conf.py ├── development.rst ├── index.rst ├── installation.rst ├── make.bat ├── requirements.txt ├── source │ └── _static │ │ └── figs │ │ └── astir.png └── tutorials │ ├── index.rst │ └── notebooks │ ├── data │ ├── cell-states.csv │ ├── cell-types.csv │ └── sample_data.csv │ ├── data_loading.ipynb │ ├── getting_started.ipynb │ └── img │ ├── celltype_protein_cluster.png │ ├── hdf5_schematics.png │ └── hierarchical_celltype_cluster.png ├── envs └── imc.yml ├── mkdocs.yml ├── mypy.ini ├── pytest.ini ├── requirements.txt ├── scripts ├── build-docs.sh ├── docs-live.sh ├── format.sh ├── lint.sh └── test.sh ├── setup.py └── tests ├── __init__.py ├── conftest.py ├── models ├── __init__.py ├── test_cellstate.py ├── test_celltype.py └── test_scdataset.py ├── output ├── test-data ├── adata_small.h5ad ├── bad_data.csv ├── bad_marker.yml ├── basel_100.loom ├── design.csv ├── jackson-2020-markers.yml ├── sce.csv ├── test-dir-read │ ├── one.csv │ └── two.csv ├── test_data.csv ├── test_rds.csv ├── test_rds.rds ├── test_rds_design.csv └── test_rds_marker.yml ├── test_astir.py ├── test_bin_astir.py ├── test_code_smell.py └── test_notebooks.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/camlab-bioml/astir/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: 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