CITATION.cff
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements-manuscript.txt
assets/images/Fig1A_pipeline_schematic.png
assets/images/Fig1B_sphere_example.png
assets/images/SPHERE-PCA_logo.png
assets/images/celegan_globe.png
assets/images/celegan_polar.png
assets/images/celegan_stripe.png
assets/images/epi_globe.png
assets/images/planarian.png
assets/images/planarian_test.png
examples/README.md
examples/anndata_workflow.py
examples/existing_pca.py
pca_sphere_projection/__init__.py
pca_sphere_projection/app.py
pca_sphere_projection/app_plots.py
pca_sphere_projection/app_processing.py
pca_sphere_projection/app_report.py
pca_sphere_projection/comparison.py
pca_sphere_projection/core.py
pca_sphere_projection/entropy.py
pca_sphere_projection/gene_geometry.py
pca_sphere_projection/io.py
pca_sphere_projection/known_regulators.py
pca_sphere_projection/pc_robustness.py
pca_sphere_projection/perturbation.py
pca_sphere_projection/preprocessing.py
pca_sphere_projection/robustness.py
pca_sphere_projection/sphere_stats.py
pca_sphere_projection/stripe.py
pca_sphere_projection/topology.py
pca_sphere_projection/data/example_configs.yaml
pca_sphere_projection/data/synthetic_pc_coordinates.csv
pca_sphere_projection/figures/__init__.py
pca_sphere_projection/figures/common.py
pca_sphere_projection/figures/fig1.py
pca_sphere_projection/figures/fig2.py
pca_sphere_projection/figures/fig3.py
pca_sphere_projection/figures/fig4.py
pca_sphere_projection/figures/supplements/__init__.py
pca_sphere_projection/figures/supplements/benchmark.py
pca_sphere_projection/figures/supplements/common.py
pca_sphere_projection/figures/supplements/planaria.py
pca_sphere_projection/figures/supplements/xenium.py
scripts/manuscript/README.md
scripts/manuscript/make_manuscript_figures.py
scripts/manuscript/make_supplement_figures.py
scripts/manuscript/smoke_test_celegan.py
sphere_pca/__init__.py
sphere_pca/cli.py
sphere_pca/core.py
sphere_pca/plotting.py
sphere_pca/result.py
sphere_pca.egg-info/PKG-INFO
sphere_pca.egg-info/SOURCES.txt
sphere_pca.egg-info/dependency_links.txt
sphere_pca.egg-info/entry_points.txt
sphere_pca.egg-info/requires.txt
sphere_pca.egg-info/top_level.txt
tests/test_comparison.py
tests/test_perturbation.py
tests/test_public_api.py
tests/test_robustness.py
tests/test_sphere_stats.py
tests/test_topology.py