AGENTS.md
AUTHORS.rst
CITATION.cff
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
llms.txt
requirements.txt
setup.cfg
setup.py
docs/Makefile
docs/api.rst
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/region_analysis.rst
docs/tutorials.rst
docs/notebooks/SKNY_paper_Sakai_et_al.ipynb
docs/notebooks/Xenium_analysis.ipynb
docs/notebooks/region_analysis.ipynb
docs/notebooks/single-TME_analysis.ipynb
skny/__init__.py
skny/pl.py
skny/pp.py
skny.egg-info/PKG-INFO
skny.egg-info/SOURCES.txt
skny.egg-info/dependency_links.txt
skny.egg-info/not-zip-safe
skny.egg-info/requires.txt
skny.egg-info/top_level.txt
skny/plotting/__init__.py
skny/plotting/clustering_heatmap.py
skny/plotting/deg_manhattan_plot.py
skny/plotting/distance_gene_plot.py
skny/plotting/equidistant_curves.py
skny/plotting/preprocessed_images.py
skny/plotting/region_density_plot.py
skny/plotting/region_map.py
skny/preprocessing/__init__.py
skny/preprocessing/calculate_region.py
skny/preprocessing/convert_indivisual_peri.py
skny/preprocessing/convert_indivisual_solid.py
skny/preprocessing/cv2pil.py
skny/preprocessing/distance_calculator.py
skny/preprocessing/region_density.py
tests/__init__.py
tests/test_grid_workflow.py
tests/test_region.py
tests/test_skny.py