├── .codecov.yaml ├── .cruft.json ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml └── workflows │ ├── build.yaml │ ├── release.yaml │ └── test.yaml ├── .gitignore ├── .ipynb_checkpoints ├── README-checkpoint.md └── pyproject-checkpoint.toml ├── .pre-commit-config.yaml ├── .prettierrc.yaml ├── .readthedocs.yaml ├── .vscode ├── extensions.json ├── launch.json └── settings.json ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── .ipynb_checkpoints │ ├── conf-checkpoint.py │ ├── contributing-checkpoint.md │ ├── index-checkpoint.md │ ├── references-checkpoint.bib │ └── references-checkpoint.md ├── Makefile ├── _static │ ├── .gitkeep │ └── css │ │ └── custom.css ├── _templates │ ├── .gitkeep │ └── autosummary │ │ └── class.rst ├── api │ ├── .ipynb_checkpoints │ │ ├── plotting-checkpoint.md │ │ ├── preprocessing-checkpoint.md │ │ └── tools-checkpoint.md │ ├── plotting.md │ ├── preprocessing.md │ └── tools.md ├── changelog.md ├── conf.py ├── contributing.md ├── extensions │ └── typed_returns.py ├── images │ └── logo_fish.png ├── index.md ├── notebooks │ ├── .ipynb_checkpoints │ │ └── Basic_tutorial-checkpoint.ipynb │ └── Basic_tutorial.ipynb ├── references.bib └── references.md ├── images └── logo_fish.png ├── notebooks └── spatialdata_tutorials │ ├── .ipynb_checkpoints │ ├── 0_format_Xenium_sdata-checkpoint.ipynb │ ├── 2_run_segmentation_free-checkpoint.ipynb │ ├── 4_quantify_exRNA-checkpoint.ipynb │ ├── 5_explore_comunication-checkpoint.ipynb │ └── run_sainsc-checkpoint.ipynb │ ├── 0_format_Xenium_sdata.ipynb │ ├── 1_segmentation.ipynb │ ├── 2_run_segmentation_free.ipynb │ ├── 3_process_cells.ipynb │ ├── 4_quantify_exRNA.ipynb │ ├── 5_explore_comunication.ipynb │ ├── 6_signature_analysis.ipynb │ ├── 7_image_quantification.ipynb │ ├── DEPRECATED_test_code.ipynb │ ├── run_sainsc.ipynb │ └── run_sainsc_4_campa.ipynb ├── output.png ├── pyproject.toml ├── src └── troutpy │ ├── .ipynb_checkpoints │ └── __init__-checkpoint.py │ ├── __init__.py │ ├── _utils.py │ ├── pl │ ├── .ipynb_checkpoints │ │ ├── __init__-checkpoint.py │ │ ├── basic-checkpoint.py │ │ ├── colors-checkpoint.py │ │ ├── communication-checkpoint.py │ │ ├── factor_analysis-checkpoint.py │ │ ├── metric_analysis-checkpoint.py │ │ ├── plotting-checkpoint.py │ │ ├── scatter-checkpoint.py │ │ └── source-checkpoint.py │ ├── __init__.py │ ├── basic.py │ ├── colors.py │ ├── communication.py │ ├── factor_analysis.py │ ├── metric_analysis.py │ ├── plotting.py │ ├── scatter.py │ └── source.py │ ├── pp │ ├── .ipynb_checkpoints │ │ ├── __init__-checkpoint.py │ │ ├── aggregate-checkpoint.py │ │ ├── compute-checkpoint.py │ │ ├── converter-checkpoint.py │ │ └── format-checkpoint.py │ ├── __init__.py │ ├── aggregate.py │ ├── compute.py │ ├── converter.py │ └── format.py │ ├── read │ └── __init__.py │ └── tl │ ├── .ipynb_checkpoints │ ├── __init__-checkpoint.py │ ├── estimate_density-checkpoint.py │ ├── factor_analysis-checkpoint.py │ ├── image_quantification-checkpoint.py │ ├── interactions-checkpoint.py │ ├── quantify_urna-checkpoint.py │ ├── segmentation_free-checkpoint.py │ ├── source_cell-checkpoint.py │ └── target_cell-checkpoint.py │ ├── __init__.py │ ├── estimate_density.py │ ├── factor_analysis.py │ ├── image_quantification.py │ ├── interactions.py │ ├── quantify_urna.py │ ├── segmentation_free.py │ ├── source_cell.py │ └── target_cell.py └── tests └── test_basic.py /.codecov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/theislab/troutpy/HEAD/.codecov.yaml -------------------------------------------------------------------------------- /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/theislab/troutpy/HEAD/.cruft.json -------------------------------------------------------------------------------- /.editorconfig: 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