LICENSE
MANIFEST.in
README.md
pyproject.toml
oncoref/__init__.py
oncoref/antigen_coverage.py
oncoref/apd1.py
oncoref/cancer_genes.py
oncoref/cancer_ontology.py
oncoref/cancer_types.py
oncoref/catalog.py
oncoref/cli.py
oncoref/cohorts.py
oncoref/coverage.py
oncoref/cta.py
oncoref/cta_coverage.py
oncoref/cta_curation_plots.py
oncoref/cta_peptides.py
oncoref/cta_regen.py
oncoref/cta_tissues.py
oncoref/data_bundle.py
oncoref/data_manifest.py
oncoref/expression.py
oncoref/expression_builders.py
oncoref/expression_engine.py
oncoref/expression_registry.py
oncoref/fusions.py
oncoref/gene_families.py
oncoref/gene_ids.py
oncoref/gene_qc.py
oncoref/genome.py
oncoref/hpa.py
oncoref/ici.py
oncoref/ici_response.py
oncoref/incidence.py
oncoref/load_dataset.py
oncoref/normalization.py
oncoref/peptides.py
oncoref/plots.py
oncoref/proteoforms.py
oncoref/reference_data.py
oncoref/response_signatures.py
oncoref/samples.py
oncoref/source_matrices.py
oncoref/tmb.py
oncoref/version.py
oncoref.egg-info/PKG-INFO
oncoref.egg-info/SOURCES.txt
oncoref.egg-info/dependency_links.txt
oncoref.egg-info/entry_points.txt
oncoref.egg-info/requires.txt
oncoref.egg-info/top_level.txt
oncoref/data/cancer-apd1-response.csv
oncoref/data/cancer-code-burden-map.csv
oncoref/data/cancer-cohort-aggregates.csv
oncoref/data/cancer-driver-genes.csv
oncoref/data/cancer-driver-variants.csv
oncoref/data/cancer-expression-source-candidates.csv
oncoref/data/cancer-frameshift-burden.csv
oncoref/data/cancer-fusions.csv
oncoref/data/cancer-ici-response-estimates.csv
oncoref/data/cancer-ici-response.csv
oncoref/data/cancer-incidence-mortality.csv
oncoref/data/cancer-key-genes.csv
oncoref/data/cancer-lineage-group-overrides.csv
oncoref/data/cancer-lineage-groups.csv
oncoref/data/cancer-mismatch-repair-statuses.csv
oncoref/data/cancer-normal-tissue-map.csv
oncoref/data/cancer-reference-expression-samples.csv.gz
oncoref/data/cancer-response-signatures.csv
oncoref/data/cancer-subtype-groupings.csv
oncoref/data/cancer-testis-antigens.csv
oncoref/data/cancer-tmb.csv
oncoref/data/cancer-type-genes.csv
oncoref/data/cancer-type-registry.csv
oncoref/data/cancer-viral-antigens.csv
oncoref/data/canonical-gene-space.csv.gz
oncoref/data/cdna-identical-gene-groups.csv
oncoref/data/censored-gene-reference-tpm.csv
oncoref/data/clean-tpm-biological-housekeeping-genes.csv
oncoref/data/clean-tpm-censored-genes.csv
oncoref/data/cohort-registry.csv
oncoref/data/cta-candidate-references.csv
oncoref/data/cta-clinical-targets.csv
oncoref/data/cta-ihc-unreliable.csv
oncoref/data/cta-specificity-audit.csv
oncoref/data/degenerate-subtype-pairs.csv
oncoref/data/disease-state-rules.csv
oncoref/data/ensembl-id-aliases.csv
oncoref/data/expression-artifact-gene-universe-deltas.csv
oncoref/data/expression_sources.yaml
oncoref/data/extra-tx-mappings.csv
oncoref/data/family-burden-map.csv
oncoref/data/fusion-expression-effects.csv
oncoref/data/fusion-surrogate-expression.csv
oncoref/data/hemoglobin-genes.csv
oncoref/data/histone-genes.csv
oncoref/data/housekeeping-genes.csv
oncoref/data/mitochondrial-genes.csv
oncoref/data/narrative-gene-sets.csv
oncoref/data/ncbi-entrez-gene-mappings.csv.gz
oncoref/data/ncbi-symbol-synonyms.csv.gz
oncoref/data/nuclear-retained-lncrnas.csv
oncoref/data/numt-pseudogenes.csv
oncoref/data/proteoform-collapse-overrides.csv
oncoref/data/proteoform-groups-genome.csv
oncoref/data/proteoform-groups.csv
oncoref/data/rare-cancer-fusion-rules.csv
oncoref/data/ribosomal-protein-genes.csv
oncoref/data/ribosomal-protein-pseudogenes.csv
oncoref/data/rrna-and-pseudogenes.csv
oncoref/data/small-noncoding-rnas.csv
oncoref/data/source-matrices.csv
oncoref/data/tissue-burden-map.csv
tests/test_apd1.py
tests/test_api_structure.py
tests/test_base_layer.py
tests/test_build_generators.py
tests/test_cancer_genes.py
tests/test_cancer_type_registry.py
tests/test_cancer_types.py
tests/test_catalog.py
tests/test_cli.py
tests/test_coverage.py
tests/test_cta.py
tests/test_cta_regen.py
tests/test_cta_table_integrity.py
tests/test_data_bundle.py
tests/test_data_manifest.py
tests/test_data_parity.py
tests/test_expression.py
tests/test_expression_engine.py
tests/test_expression_sources.py
tests/test_exprmeta.py
tests/test_fusions.py
tests/test_gene_families.py
tests/test_gene_ids.py
tests/test_gene_qc.py
tests/test_genome.py
tests/test_genome_pick.py
tests/test_hpa.py
tests/test_ici.py
tests/test_ici_estimates.py
tests/test_incidence.py
tests/test_normalization.py
tests/test_ontology_hierarchy_curation.py
tests/test_peptides.py
tests/test_plots.py
tests/test_proteoform_genome.py
tests/test_proteoforms.py
tests/test_reference_data.py
tests/test_release_workflow.py
tests/test_response_signatures.py
tests/test_samples.py
tests/test_source_matrices.py
tests/test_subtype_groupings.py
tests/test_tmb.py
tests/test_tree_navigation.py
tests/test_within_sample.py
tests/test_within_sample_proteoform.py