LICENSE
README.md
pyproject.toml
src/bioprocess_mir/__init__.py
src/bioprocess_mir/cli.py
src/bioprocess_mir/concept_resolution.py
src/bioprocess_mir/evidence.py
src/bioprocess_mir/mirna_targets.py
src/bioprocess_mir/process_genes.py
src/bioprocess_mir/py.typed
src/bioprocess_mir/summary.py
src/bioprocessdb/__init__.py
src/bioprocessdb/checksum.py
src/bioprocessdb/cli.py
src/bioprocessdb/config.py
src/bioprocessdb/database.py
src/bioprocessdb/downloader.py
src/bioprocessdb/exceptions.py
src/bioprocessdb/logging_utils.py
src/bioprocessdb/manifests.py
src/bioprocessdb/optional_deps.py
src/bioprocessdb/py.typed
src/bioprocessdb/query.py
src/bioprocessdb/schema_version.py
src/bioprocessdb/validation.py
src/bioprocessdb/workflow.py
src/bioprocessdb.egg-info/PKG-INFO
src/bioprocessdb.egg-info/SOURCES.txt
src/bioprocessdb.egg-info/dependency_links.txt
src/bioprocessdb.egg-info/entry_points.txt
src/bioprocessdb.egg-info/requires.txt
src/bioprocessdb.egg-info/top_level.txt
src/bioprocessdb/default_config/default.yaml
src/bioprocessdb/default_config/go_evidence_mapping.yaml
src/bioprocessdb/default_config/logging.yaml
src/bioprocessdb/default_config/mirtarbase_column_aliases.yaml
src/bioprocessdb/default_config/mirtarbase_evidence_mapping.yaml
src/bioprocessdb/default_config/sources.yaml
src/bioprocessdb/enrichment/__init__.py
src/bioprocessdb/enrichment/cache.py
src/bioprocessdb/enrichment/contingency.py
src/bioprocessdb/enrichment/effect_sizes.py
src/bioprocessdb/enrichment/export.py
src/bioprocessdb/enrichment/models.py
src/bioprocessdb/enrichment/multiple_testing.py
src/bioprocessdb/enrichment/provenance.py
src/bioprocessdb/enrichment/query_spec.py
src/bioprocessdb/enrichment/sensitivity.py
src/bioprocessdb/enrichment/service.py
src/bioprocessdb/enrichment/statistics.py
src/bioprocessdb/enrichment/target_sets.py
src/bioprocessdb/enrichment/universe.py
src/bioprocessdb/enrichment/validation.py
src/bioprocessdb/enrichment/versions.py
src/bioprocessdb/go/__init__.py
src/bioprocessdb/go/build_go.py
src/bioprocessdb/go/evidence.py
src/bioprocessdb/go/gaf_parser.py
src/bioprocessdb/go/gene_mapping.py
src/bioprocessdb/go/membership.py
src/bioprocessdb/go/obo_parser.py
src/bioprocessdb/go/ontology.py
src/bioprocessdb/go/qc.py
src/bioprocessdb/identifiers/__init__.py
src/bioprocessdb/identifiers/augment.py
src/bioprocessdb/identifiers/build_genes.py
src/bioprocessdb/identifiers/build_xrefs.py
src/bioprocessdb/identifiers/ensembl_parser.py
src/bioprocessdb/identifiers/hgnc_parser.py
src/bioprocessdb/identifiers/mapping.py
src/bioprocessdb/identifiers/normalize.py
src/bioprocessdb/identifiers/resolver.py
src/bioprocessdb/identifiers/schemas.py
src/bioprocessdb/identifiers/uniprot_parser.py
src/bioprocessdb/kegg/__init__.py
src/bioprocessdb/kegg/build_kegg.py
src/bioprocessdb/kegg/mapping.py
src/bioprocessdb/kegg/parsers.py
src/bioprocessdb/kegg/pathway_source.py
src/bioprocessdb/kegg/qc.py
src/bioprocessdb/knowledge/__init__.py
src/bioprocessdb/knowledge/go_adapter.py
src/bioprocessdb/mirtarbase/__init__.py
src/bioprocessdb/mirtarbase/build_mirtarbase.py
src/bioprocessdb/mirtarbase/build_tables.py
src/bioprocessdb/mirtarbase/evidence.py
src/bioprocessdb/mirtarbase/interaction_source.py
src/bioprocessdb/mirtarbase/mirna_normalize.py
src/bioprocessdb/mirtarbase/parsers.py
src/bioprocessdb/mirtarbase/qc.py
src/bioprocessdb/prioritization/__init__.py
src/bioprocessdb/prioritization/cache.py
src/bioprocessdb/prioritization/comparison.py
src/bioprocessdb/prioritization/components.py
src/bioprocessdb/prioritization/eligibility.py
src/bioprocessdb/prioritization/export.py
src/bioprocessdb/prioritization/models.py
src/bioprocessdb/prioritization/ordering.py
src/bioprocessdb/prioritization/pareto.py
src/bioprocessdb/prioritization/policies.py
src/bioprocessdb/prioritization/provenance.py
src/bioprocessdb/prioritization/query_spec.py
src/bioprocessdb/prioritization/sensitivity.py
src/bioprocessdb/prioritization/service.py
src/bioprocessdb/prioritization/tiers.py
src/bioprocessdb/prioritization/validation.py
src/bioprocessdb/prioritization/versions.py
src/bioprocessdb/prioritization/weighted.py
src/bioprocessdb/process_engine/__init__.py
src/bioprocessdb/process_engine/aggregation.py
src/bioprocessdb/process_engine/cache.py
src/bioprocessdb/process_engine/candidates.py
src/bioprocessdb/process_engine/expansion.py
src/bioprocessdb/process_engine/export.py
src/bioprocessdb/process_engine/gene_sets.py
src/bioprocessdb/process_engine/models.py
src/bioprocessdb/process_engine/provenance.py
src/bioprocessdb/process_engine/query_spec.py
src/bioprocessdb/process_engine/search.py
src/bioprocessdb/process_engine/selection.py
src/bioprocessdb/process_engine/service.py
src/bioprocessdb/process_engine/validation.py
src/bioprocessdb/process_engine/versions.py
src/bioprocessdb/process_mirna/__init__.py
src/bioprocessdb/process_mirna/cache.py
src/bioprocessdb/process_mirna/candidates.py
src/bioprocessdb/process_mirna/coverage.py
src/bioprocessdb/process_mirna/evidence.py
src/bioprocessdb/process_mirna/export.py
src/bioprocessdb/process_mirna/linker.py
src/bioprocessdb/process_mirna/models.py
src/bioprocessdb/process_mirna/provenance.py
src/bioprocessdb/process_mirna/query_spec.py
src/bioprocessdb/process_mirna/service.py
src/bioprocessdb/process_mirna/validation.py
src/bioprocessdb/process_mirna/versions.py
src/bioprocessdb/providers/__init__.py
src/bioprocessdb/providers/base.py
src/bioprocessdb/providers/ensembl.py
src/bioprocessdb/providers/go.py
src/bioprocessdb/providers/hgnc.py
src/bioprocessdb/providers/kegg.py
src/bioprocessdb/providers/mirtarbase.py
src/bioprocessdb/providers/quickgo.py
src/bioprocessdb/providers/reactome.py
src/bioprocessdb/providers/registry.py
src/bioprocessdb/providers/uniprot.py
src/bioprocessdb/providers/wikipathways.py
src/bioprocessdb/reactome/__init__.py
src/bioprocessdb/reactome/build_reactome.py
src/bioprocessdb/reactome/hierarchy.py
src/bioprocessdb/reactome/mapping.py
src/bioprocessdb/reactome/membership.py
src/bioprocessdb/reactome/parsers.py
src/bioprocessdb/reactome/pathway_source.py
src/bioprocessdb/reactome/qc.py
src/bioprocessdb/reporting/__init__.py
src/bioprocessdb/reporting/cache.py
src/bioprocessdb/reporting/comparison.py
src/bioprocessdb/reporting/context.py
src/bioprocessdb/reporting/export.py
src/bioprocessdb/reporting/html.py
src/bioprocessdb/reporting/interpretation.py
src/bioprocessdb/reporting/machine_readable.py
src/bioprocessdb/reporting/markdown.py
src/bioprocessdb/reporting/models.py
src/bioprocessdb/reporting/narrative.py
src/bioprocessdb/reporting/plots.py
src/bioprocessdb/reporting/provenance.py
src/bioprocessdb/reporting/renderers.py
src/bioprocessdb/reporting/service.py
src/bioprocessdb/reporting/tables.py
src/bioprocessdb/reporting/templates.py
src/bioprocessdb/reporting/themes.py
src/bioprocessdb/reporting/validation.py
src/bioprocessdb/reporting/versions.py
src/bioprocessdb/unified/__init__.py
src/bioprocessdb/unified/build_database.py
src/bioprocessdb/unified/export.py
src/bioprocessdb/unified/manifest.py
src/bioprocessdb/unified/qc.py
src/bioprocessdb/unified/record_keys.py
src/bioprocessdb/unified/registry.py
src/bioprocessdb/unified/search.py
src/bioprocessdb/unified/validation.py
src/bioprocessdb/unified/views.py
src/bioprocessdb/wikipathways/__init__.py
src/bioprocessdb/wikipathways/build_wikipathways.py
src/bioprocessdb/wikipathways/mapping.py
src/bioprocessdb/wikipathways/parsers.py
src/bioprocessdb/wikipathways/pathway_source.py
src/bioprocessdb/wikipathways/qc.py