LICENSE
README.md
pyproject.toml
src/pyXenium/__init__.py
src/pyXenium/__main__.py
src/pyXenium/_compat.py
src/pyXenium/_topology_core.py
src/pyXenium/_version.py
src/pyXenium.egg-info/PKG-INFO
src/pyXenium.egg-info/SOURCES.txt
src/pyXenium.egg-info/dependency_links.txt
src/pyXenium.egg-info/entry_points.txt
src/pyXenium.egg-info/requires.txt
src/pyXenium.egg-info/top_level.txt
src/pyXenium/analysis/__init__.py
src/pyXenium/analysis/differential.py
src/pyXenium/analysis/ligand_receptor_topology.py
src/pyXenium/analysis/microenv_analysis.py
src/pyXenium/analysis/pathway_topology.py
src/pyXenium/analysis/plotting.py
src/pyXenium/analysis/protein_gene_correlation.py
src/pyXenium/analysis/protein_microenvironment.py
src/pyXenium/analysis/rna_protein_cluster_analysis.py
src/pyXenium/analysis/scoring.py
src/pyXenium/analysis/spatial_immune_resistance.py
src/pyXenium/analysis/tabnet_model.py
src/pyXenium/analysis/tabnet_pipeline.py
src/pyXenium/analysis/tabnet_reports.py
src/pyXenium/analysis/tabnet_tools.py
src/pyXenium/config/protein_aliases.yaml
src/pyXenium/contour/__init__.py
src/pyXenium/contour/_analysis.py
src/pyXenium/contour/_geometry.py
src/pyXenium/contour/_transform.py
src/pyXenium/contour/loading.py
src/pyXenium/datasets/__init__.py
src/pyXenium/datasets/catalog.py
src/pyXenium/datasets/toy_slide/__init__.py
src/pyXenium/datasets/toy_slide/analysis.zarr.zip
src/pyXenium/datasets/toy_slide/cells.zarr.zip
src/pyXenium/datasets/toy_slide/transcripts.zarr.zip
src/pyXenium/io/__init__.py
src/pyXenium/io/api.py
src/pyXenium/io/io.py
src/pyXenium/io/partial_xenium_loader.py
src/pyXenium/io/sdata_model.py
src/pyXenium/io/sdata_store.py
src/pyXenium/io/spatialdata_export.py
src/pyXenium/io/xenium_artifacts.py
src/pyXenium/io/xenium_gene_protein_loader.py
src/pyXenium/ligand_receptor/__init__.py
src/pyXenium/ligand_receptor/_analysis.py
src/pyXenium/multimodal/__init__.py
src/pyXenium/multimodal/immune_resistance.py
src/pyXenium/multimodal/loading.py
src/pyXenium/multimodal/analysis/__init__.py
src/pyXenium/multimodal/analysis/differential.py
src/pyXenium/multimodal/analysis/microenv_analysis.py
src/pyXenium/multimodal/analysis/plotting.py
src/pyXenium/multimodal/analysis/protein_gene_correlation.py
src/pyXenium/multimodal/analysis/protein_microenvironment.py
src/pyXenium/multimodal/analysis/rna_protein_cluster_analysis.py
src/pyXenium/multimodal/analysis/scoring.py
src/pyXenium/multimodal/analysis/tabnet_model.py
src/pyXenium/multimodal/analysis/tabnet_pipeline.py
src/pyXenium/multimodal/analysis/tabnet_reports.py
src/pyXenium/multimodal/analysis/tabnet_tools.py
src/pyXenium/multimodal/workflows/__init__.py
src/pyXenium/multimodal/workflows/renal_ffpe_protein.py
src/pyXenium/multimodal/workflows/renal_immune_resistance.py
src/pyXenium/pathway/__init__.py
src/pyXenium/pathway/_analysis.py
src/pyXenium/utils/name_resolver.py
src/pyXenium/validation/__init__.py
src/pyXenium/validation/atera_wta_breast_topology.py
src/pyXenium/validation/renal_ffpe_protein.py
src/pyXenium/validation/renal_immune_resistance.py
src/pyXenium/vis/fig_microenv.py
tests/test_cli.py
tests/test_contour_module.py
tests/test_dataset_catalog.py
tests/test_multimodal_module.py
tests/test_spatial_immune_resistance.py
tests/test_topology_analysis.py
tests/test_validation_module.py
tests/test_xenium_io.py