CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
configs/example_autism.yaml
configs/example_epilepsy.yaml
configs/example_expression.yaml
configs/example_intellectual_disability.yaml
configs/example_schizophrenia.yaml
configs/sepsis_gse65682.yaml
configs/sepsis_gse65682_k4.yaml
configs/test_synthetic.yaml
data/pathways/README.md
data/pathways/autism_pathways.gmt
data/pathways/bipolar_pathways.gmt
data/pathways/epilepsy_pathways.gmt
data/pathways/hallmark_200genes.gmt
data/pathways/intellectual_disability_pathways.gmt
data/pathways/parkinsons_pathways.gmt
data/pathways/schizophrenia_pathways.gmt
data/sample/synthetic_cohort.vcf
data/sample/synthetic_phenotypes.csv
docs/CODEBERG-ISSUES-ROADMAP.md
docs/METHODS.md
docs/data_formats.md
docs/framework_overview.md
docs/gap-validation-implementation-plan.md
docs/how-it-works.md
docs/limitations.md
docs/molecular-qc-test-plan.md
docs/notebook-guide.md
docs/ocircuit-bpu-adaptation-plan.md
docs/one-pager-template.md
docs/one-pager.md
docs/outputs_dictionary.md
docs/project-roadmap.md
docs/provenance.md
docs/quickstart.md
docs/real-data-acceptance-f2-f5-f10.md
docs/reproducibility.md
docs/roadmap-molecular-qc-v05.md
docs/roadmap-v06-codeberg.md
docs/roadmap-v07-bpu-private.md
docs/tcga-acc-extension.md
docs/terminology.md
docs/troubleshooting.md
docs/zenodo_setup.md
docs/api/ancestry.md
docs/api/autism.md
docs/api/batch_correction.md
docs/api/benchmark.md
docs/api/characterization.md
docs/api/cli.md
docs/api/clustering.md
docs/api/config.md
docs/api/cross_cohort.md
docs/api/cross_modal_validation.md
docs/api/deconvolution.md
docs/api/expression.md
docs/api/gnn.md
docs/api/index.md
docs/api/multi_omic.md
docs/api/pipeline.md
docs/api/qc.md
docs/api/sensitivity.md
docs/api/signaling_databases.md
docs/api/simulation.md
docs/api/single_cell.md
docs/api/statistical_rigor.md
docs/api/threshold_calibration.md
docs/api/validation.md
docs/api/variant_qc.md
docs/api/visualization.md
docs/collaboration/email-template.md
docs/collaboration/target-labs.md
docs/contributor-kit/01-getting-started.md
docs/contributor-kit/02-data-access-guide.md
docs/contributor-kit/04-research-compliance.md
docs/contributor-kit/05-project-proposal-template.md
docs/contributor-kit/06-technical-setup.md
docs/contributor-kit/07-analysis-workflow.md
docs/contributor-kit/08-publishing-guidelines.md
docs/contributor-kit/09-faq.md
docs/contributor-kit/README.md
docs/contributor-kit/03-data-sources/clinvar-usage-guide.md
docs/contributor-kit/03-data-sources/dbgap-application-template.md
docs/contributor-kit/03-data-sources/gnomad-usage-guide.md
docs/contributor-kit/03-data-sources/sfari-application-template.md
docs/contributor-kit/03-data-sources/ukbiobank-application-template.md
docs/guides/adapting-for-your-disease.md
docs/guides/contributing-pathways.md
docs/guides/cross-cohort-validation.md
docs/guides/cross-platform.md
docs/guides/embeddings.md
docs/guides/pathway-curation-guide.md
docs/guides/performance-and-hardware.md
docs/guides/perturbation.md
docs/guides/uncertainty.md
docs/guides/validation-gates.md
docs/migration/v05-to-v06-kg.md
src/pathway_subtyping/__init__.py
src/pathway_subtyping/__main__.py
src/pathway_subtyping/ancestry.py
src/pathway_subtyping/batch_correction.py
src/pathway_subtyping/benchmark.py
src/pathway_subtyping/characterization.py
src/pathway_subtyping/cli.py
src/pathway_subtyping/clustering.py
src/pathway_subtyping/config.py
src/pathway_subtyping/cross_cohort.py
src/pathway_subtyping/cross_modal_validation.py
src/pathway_subtyping/data_quality.py
src/pathway_subtyping/deconvolution.py
src/pathway_subtyping/expression.py
src/pathway_subtyping/multi_omic.py
src/pathway_subtyping/network_propagation.py
src/pathway_subtyping/pipeline.py
src/pathway_subtyping/py.typed
src/pathway_subtyping/sensitivity.py
src/pathway_subtyping/signaling_databases.py
src/pathway_subtyping/simulation.py
src/pathway_subtyping/single_cell.py
src/pathway_subtyping/statistical_rigor.py
src/pathway_subtyping/threshold_calibration.py
src/pathway_subtyping/validation.py
src/pathway_subtyping/validation_datasets.py
src/pathway_subtyping/variant_qc.py
src/pathway_subtyping/visualization.py
src/pathway_subtyping.egg-info/PKG-INFO
src/pathway_subtyping.egg-info/SOURCES.txt
src/pathway_subtyping.egg-info/dependency_links.txt
src/pathway_subtyping.egg-info/entry_points.txt
src/pathway_subtyping.egg-info/requires.txt
src/pathway_subtyping.egg-info/top_level.txt
src/pathway_subtyping/active/__init__.py
src/pathway_subtyping/active/selector.py
src/pathway_subtyping/autism/__init__.py
src/pathway_subtyping/autism/neurosymbolic/__init__.py
src/pathway_subtyping/autism/neurosymbolic/combiner.py
src/pathway_subtyping/autism/rules/__init__.py
src/pathway_subtyping/autism/rules/biological_rules.py
src/pathway_subtyping/autism/rules/conditions.py
src/pathway_subtyping/autism/rules/engine.py
src/pathway_subtyping/autism/rules/explanation.py
src/pathway_subtyping/autism/therapeutic/__init__.py
src/pathway_subtyping/autism/therapeutic/drug_mapping.py
src/pathway_subtyping/autism/therapeutic/evidence.py
src/pathway_subtyping/autism/therapeutic/ranking.py
src/pathway_subtyping/causal/__init__.py
src/pathway_subtyping/causal/invariant.py
src/pathway_subtyping/data/pathways/autism_pathways.gmt
src/pathway_subtyping/data/pathways/bipolar_pathways.gmt
src/pathway_subtyping/data/pathways/epilepsy_pathways.gmt
src/pathway_subtyping/data/pathways/intellectual_disability_pathways.gmt
src/pathway_subtyping/data/pathways/parkinsons_pathways.gmt
src/pathway_subtyping/data/pathways/schizophrenia_pathways.gmt
src/pathway_subtyping/embed/__init__.py
src/pathway_subtyping/embed/base.py
src/pathway_subtyping/embed/cache.py
src/pathway_subtyping/embed/nicheformer.py
src/pathway_subtyping/embed/scgpt.py
src/pathway_subtyping/genesets/__init__.py
src/pathway_subtyping/genesets/regulatory.py
src/pathway_subtyping/gnn/__init__.py
src/pathway_subtyping/gnn/attention.py
src/pathway_subtyping/gnn/config.py
src/pathway_subtyping/gnn/kg_embeddings.py
src/pathway_subtyping/gnn/layers.py
src/pathway_subtyping/gnn/model.py
src/pathway_subtyping/gnn/embeddings/__init__.py
src/pathway_subtyping/gnn/embeddings/fusion.py
src/pathway_subtyping/harmonize/__init__.py
src/pathway_subtyping/harmonize/align.py
src/pathway_subtyping/harmonize/benchmark.py
src/pathway_subtyping/harmonize/confidence.py
src/pathway_subtyping/harmonize/uce.py
src/pathway_subtyping/knowledge_graph/__init__.py
src/pathway_subtyping/knowledge_graph/builder.py
src/pathway_subtyping/knowledge_graph/diff.py
src/pathway_subtyping/knowledge_graph/exporters.py
src/pathway_subtyping/knowledge_graph/regression.py
src/pathway_subtyping/knowledge_graph/schema.py
src/pathway_subtyping/knowledge_graph/sources.py
src/pathway_subtyping/omics/__init__.py
src/pathway_subtyping/omics/atac.py
src/pathway_subtyping/omics/discordance.py
src/pathway_subtyping/omics/fusion.py
src/pathway_subtyping/omics/proteomics.py
src/pathway_subtyping/perturb/__init__.py
src/pathway_subtyping/perturb/geneformer_wrapper.py
src/pathway_subtyping/perturb/msv_from_embedding.py
src/pathway_subtyping/perturb/report.py
src/pathway_subtyping/perturb/screen.py
src/pathway_subtyping/qc/__init__.py
src/pathway_subtyping/qc/alphamissense.py
src/pathway_subtyping/qc/atlas.py
src/pathway_subtyping/qc/cascade.py
src/pathway_subtyping/qc/crosstalk.py
src/pathway_subtyping/qc/dosage.py
src/pathway_subtyping/qc/drift.py
src/pathway_subtyping/qc/feedback.py
src/pathway_subtyping/qc/gates.py
src/pathway_subtyping/qc/heterogeneity.py
src/pathway_subtyping/qc/offtarget.py
src/pathway_subtyping/qc/offtarget_sequence.py
src/pathway_subtyping/qc/stress.py
src/pathway_subtyping/qc/temporal.py
src/pathway_subtyping/qc/tension.py
src/pathway_subtyping/qc/testing/__init__.py
src/pathway_subtyping/qc/testing/orthogonality.py
src/pathway_subtyping/qc/testing/severity_titration.py
src/pathway_subtyping/qc/testing/simulator.py
src/pathway_subtyping/qc/testing/fixtures/cart_spec.yaml
src/pathway_subtyping/qc/testing/fixtures/feedback_loops.yaml
src/pathway_subtyping/qc/testing/fixtures/healthy_batch_spec.yaml
src/pathway_subtyping/qc/testing/fixtures/stress_signatures.yaml
src/pathway_subtyping/qc/testing/fixtures/therapeutic_windows.yaml
src/pathway_subtyping/qc/testing/prospective/__init__.py
src/pathway_subtyping/qc/testing/retrospective/__init__.py
src/pathway_subtyping/qc/testing/scenarios/__init__.py
src/pathway_subtyping/qc/testing/scenarios/base.py
src/pathway_subtyping/qc/testing/scenarios/cart_manufacturing.py
src/pathway_subtyping/qc/testing/scenarios/passage_stability.py
src/pathway_subtyping/qc/testing/scenarios/report_validator.py
src/pathway_subtyping/uncertainty/__init__.py
src/pathway_subtyping/uncertainty/bayesian_pathway.py
src/pathway_subtyping/uncertainty/bootstrap.py
src/pathway_subtyping/uncertainty/calibration.py
src/pathway_subtyping/uncertainty/conformal.py
src/pathway_subtyping/utils/__init__.py
src/pathway_subtyping/utils/performance.py
src/pathway_subtyping/utils/seed.py