CHANGELOG.md
LICENSE
MANIFEST.in
README.md
deploy.sh
develop.sh
lint.sh
mkdocs.yml
pyproject.toml
requirements.txt
test.sh
.github/workflows/docs.yml
.github/workflows/tests.yml
docs/api.md
docs/cached.md
docs/consumer-guide.md
docs/expression-semantics.md
docs/fragments.md
docs/index.md
docs/osteosarc-rna-audit.md
docs/osteosarc-rna-overlay.md
docs/osteosarc-shared-data.md
docs/osteosarc-variant-outcomes.md
docs/properties.md
docs/pvacseq.md
docs/quickstart.md
docs/ranking.md
docs/self_proteome.md
docs/specs/fragment-identity-collisions.md
docs/specs/fragment-identity-from-producers.md
docs/specs/osteosarc-all-variant-outcomes.md
docs/specs/osteosarc-continuity-and-shared-inputs.md
docs/specs/osteosarc-rna-overlay.md
scripts/download_verified.sh
scripts/osteosarc_rna_overlay.py
scripts/osteosarc_test_data.py
scripts/osteosarc_variant_audit.py
scripts/resolve_python.sh
tests/__init__.py
tests/check_distributions.py
tests/combine_coverage.py
tests/common.py
tests/conftest.py
tests/data.py
tests/optional_dependencies.py
tests/osteosarc_all_helpers.py
tests/osteosarc_helpers.py
tests/osteosarc_overlay_helpers.py
tests/pvacseq_corpus_helpers.py
tests/test_absent_vs_empty_audit.py
tests/test_allele_class.py
tests/test_allele_free_kinds.py
tests/test_allele_set.py
tests/test_amino_acids.py
tests/test_annotations.py
tests/test_args_outputs.py
tests/test_best_allele.py
tests/test_cache_allele_nulls.py
tests/test_cache_key_allele_set.py
tests/test_cached_predictor.py
tests/test_cached_protein_scan_context.py
tests/test_canonical_methods.py
tests/test_ci_coverage.py
tests/test_cli_cached_predictor.py
tests/test_cli_coverage.py
tests/test_cli_protein_changes.py
tests/test_cli_ranking.py
tests/test_cli_script.py
tests/test_collection.py
tests/test_combine_predictor_results.py
tests/test_consumer_workflows.py
tests/test_contains_mutant_residues.py
tests/test_context_forwarding.py
tests/test_coverage_gaps.py
tests/test_cross_sample_evidence.py
tests/test_dataframe.py
tests/test_default_versions.py
tests/test_deploy_script.py
tests/test_direct_input_regressions.py
tests/test_dsl_extensions.py
tests/test_dsl_polish.py
tests/test_dsl_roundtrip.py
tests/test_edge_case_fixtures.py
tests/test_effect_expression_filters.py
tests/test_empty_and_collision_guards.py
tests/test_end_to_end.py
tests/test_epitopes_from_commandline_args.py
tests/test_evidence.py
tests/test_expression_integration.py
tests/test_expression_loader.py
tests/test_fragment_evidence.py
tests/test_fragment_paths.py
tests/test_frameshift_fragments.py
tests/test_from_predictions.py
tests/test_gate_scripts.py
tests/test_group_keys.py
tests/test_half_life_dsl_reachability.py
tests/test_inputs.py
tests/test_integration.py
tests/test_io.py
tests/test_io_lens.py
tests/test_io_pvacseq.py
tests/test_isovar_outcomes.py
tests/test_isovar_run.py
tests/test_kind_mhc_dependence.py
tests/test_kind_support.py
tests/test_lazy_imports.py
tests/test_lens_binding_override.py
tests/test_lens_multi_version.py
tests/test_lens_versions.py
tests/test_load_cufflinks_fpkm.py
tests/test_load_stringtie_gtf_fpkm.py
tests/test_mutant_epitope_predictions_class1.py
tests/test_mutant_epitope_predictions_class2.py
tests/test_named_allele_projection.py
tests/test_optional_integration_selection.py
tests/test_osteosarc_all_variants.py
tests/test_osteosarc_audit_continuity.py
tests/test_osteosarc_audit_inventory.py
tests/test_osteosarc_indels.py
tests/test_osteosarc_rearrangements.py
tests/test_osteosarc_rna_overlay.py
tests/test_osteosarc_shared.py
tests/test_padding.py
tests/test_peptide_mutation_interval.py
tests/test_peptide_property_node.py
tests/test_peptide_view.py
tests/test_per_peptide_alleles.py
tests/test_predict_from_fragments.py
tests/test_predict_from_variants_refactor.py
tests/test_prediction_columns.py
tests/test_predictor_internals.py
tests/test_protein_fragment.py
tests/test_public_helpers.py
tests/test_pvacseq_corpus.py
tests/test_ranking.py
tests/test_release.py
tests/test_result.py
tests/test_rna_evidence_units.py
tests/test_rna_helpers.py
tests/test_scoped_filters.py
tests/test_self_nearest_population.py
tests/test_self_proteome.py
tests/test_sequence_helpers.py
tests/test_serialization.py
tests/test_shared_context.py
tests/test_shared_expression_vocabulary.py
tests/test_sort_ordering.py
tests/test_sources.py
tests/test_sources_optional.py
tests/test_symmetric_evidence.py
tests/test_twin_conformance.py
tests/test_validation_and_edge_cases.py
tests/test_variant_expression_filters.py
tests/test_wide.py
tests/test_wide_structured_annotations.py
tests/data/B16-StringTie-chr1-subset.gtf
tests/data/BLOSUM62.ncbi
tests/data/genes.fpkm_tracking
tests/data/isoforms.fpkm_tracking
tests/data/isovar_output.tsv
tests/data/kallisto_abundance.tsv
tests/data/salmon_quant.sf
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tests/data/lens/sample_v1_5_1.tsv
tests/data/lens/sample_v1_9.tsv
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tests/data/osteosarc/README.md
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tests/data/osteosarc/manifest.json
tests/data/osteosarc/ont_t1.sam.gz
tests/data/osteosarc/selection.json
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tests/data/osteosarc/protein_reference/reference.pep.fa.gz
tests/data/osteosarc_all_variants/README.md
tests/data/osteosarc_all_variants/checked-inventory.json
tests/data/osteosarc_all_variants/expected.json
tests/data/osteosarc_all_variants/inventory.json
tests/data/osteosarc_all_variants/manifest.json
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topiary/ranking/nodes.py
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topiary/rna/common.py
topiary/rna/cufflinks.py
topiary/rna/expression_loader.py
topiary/rna/gtf.py