LICENSE
MANIFEST.in
README.md
pyproject.toml
CITEgeist/__init__.py
CITEgeist/examples/README.md
CITEgeist/examples/run_cuopt_qp_patient.py
CITEgeist/examples/run_module12_discovery.py
CITEgeist/examples/run_module3_unified.py
CITEgeist/examples/run_module4_discovery.py
CITEgeist/examples/run_module4b_bivariate.py
CITEgeist/examples/run_module5_integration.py
CITEgeist/examples/run_single_cell_assignment.py
CITEgeist/model/__init__.py
CITEgeist/model/checkpoints.py
CITEgeist/model/citegeist_model.py
CITEgeist/model/marker_utils.py
CITEgeist/model/module2_proposal_builder.py
CITEgeist/model/unified_config.py
CITEgeist/model/utils.py
CITEgeist/model/annotation/__init__.py
CITEgeist/model/annotation/coverage_check.py
CITEgeist/model/annotation/functional_annotation.py
CITEgeist/model/annotation/module3_5_benchmark.py
CITEgeist/model/annotation/module3_5_projection.py
CITEgeist/model/annotation/subtype_splitting.py
CITEgeist/model/assignment/__init__.py
CITEgeist/model/assignment/cell_assignment.py
CITEgeist/model/assignment/cellularity_utils.py
CITEgeist/model/assignment/single_cell_output.py
CITEgeist/model/deconvolution/__init__.py
CITEgeist/model/deconvolution/detection.py
CITEgeist/model/deconvolution/detection_refinement.py
CITEgeist/model/deconvolution/emission_init.py
CITEgeist/model/deconvolution/qp_solver.py
CITEgeist/model/discovery/__init__.py
CITEgeist/model/discovery/marker_interest.py
CITEgeist/model/discovery/spatial_colocalization.py
CITEgeist/model/gex/__init__.py
CITEgeist/model/gex/cell_level_gex.py
CITEgeist/model/gex/gex_modules.py
CITEgeist/model/gex/sace_gex.py
CITEgeist/model/morphology/__init__.py
CITEgeist/model/morphology/morphology_features.py
CITEgeist/model/morphology/nucleus_scores.py
CITEgeist/model/morphology/segmentation.py
CITEgeist/model/morphology/segmentation_qc.py
CITEgeist/model/morphology/soft_label_classifier.py
CITEgeist/model/programs/__init__.py
CITEgeist/model/programs/anchored_program_discovery.py
CITEgeist/model/programs/cross_sample_integration.py
CITEgeist/model/qc/__init__.py
CITEgeist/model/qc/_types.py
CITEgeist/model/qc/canonical_markers.py
CITEgeist/model/qc/gex_qc.py
CITEgeist/model/qc/marker_enrichment.py
CITEgeist/model/qc/proportion_qc.py
CITEgeist/model/qc/report.py
CITEgeist/model/qc/single_cell_qc.py
citegeist.egg-info/PKG-INFO
citegeist.egg-info/SOURCES.txt
citegeist.egg-info/dependency_links.txt
citegeist.egg-info/requires.txt
citegeist.egg-info/top_level.txt