ALLELE_VALIDATION.md
CLEAVAGE_AUDIT.md
CONSTRUCT_AUDIT.md
CONSTRUCT_PROCESSING.md
LICENSE
MANIFEST.in
README.md
TEST_DATA.md
requirements.txt
setup.py
examples/osteosarc_test_data/build.py
examples/osteosarc_test_data/pin_catalog.py
examples/osteosarc_test_data/recipe/catalog.json
examples/osteosarc_test_data/recipe/selection.json.gz
examples/osteosarc_test_data/recipe/fusion/ATP5MG--KMT2A.input.json
examples/osteosarc_test_data/recipe/fusion/TPST1--CRCP-T1.input.json
examples/osteosarc_test_data/recipe/headers/096fa4cbee49b53b51e321e246d5ab5e1ee96d3cb94c27d70e73e962398db0dd.sam.gz
examples/osteosarc_test_data/recipe/headers/12bddcc88cb2b6ad0ca44ba6db387afe366e643f902336847c7fa345da3fe10a.sam.gz
examples/osteosarc_test_data/recipe/headers/17cec83627e68c980f07bc210e8139337ebf2e619312f7938ae3c74e9649b1cb.sam.gz
examples/osteosarc_test_data/recipe/headers/3597564cbde476029dac7edca2dad3855fa5aca3f73bb100c8bdba11ccef377c.sam.gz
examples/osteosarc_test_data/recipe/headers/4bd8902e10b9d437224ee4a0fa2ff99660af4fe1e93ec673cbe6a28d56fbf701.sam.gz
examples/osteosarc_test_data/recipe/headers/7ce75794c282e5fce2d83e20c23ed4a62cff6a7bb0b70b933ce7be47982dec68.sam.gz
examples/osteosarc_test_data/recipe/headers/8b0fa14377364944a6636c7950de8470cd82c36ade41767abb4e6470052bba17.sam.gz
examples/osteosarc_test_data/recipe/headers/931b560e7c39d5cdd3505e0a71039e3685ba603f9b7064ea06b7d6a19363c842.sam.gz
examples/osteosarc_test_data/recipe/headers/d131a38d05ec00dd067e7e781b1899255f981b523f87a641e720a7bc4106bf26.sam.gz
examples/osteosarc_test_data/recipe/headers/d9e49ea876c4392385dbf2dd29dc6b4eee1258632e831d5265d7edc40bdc81ad.sam.gz
examples/osteosarc_test_data/recipe/headers/da31670ef867c22ddbb8b8acbb9628f34578ff7498ac6a723ad562adbb77c5b7.sam.gz
examples/osteosarc_test_data/recipe/support/osteosarc/manifest.json
examples/osteosarc_test_data/recipe/support/osteosarc/selection.json
examples/osteosarc_test_data/recipe/support/osteosarc/protein_reference/protein_reference_manifest.json
examples/osteosarc_test_data/recipe/support/osteosarc/protein_reference/reference.cdna.fa.gz
examples/osteosarc_test_data/recipe/support/osteosarc/protein_reference/reference.gtf.gz
examples/osteosarc_test_data/recipe/support/osteosarc/protein_reference/reference.pep.fa.gz
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/documented.json
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/netmhcpan42.tsv
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/predictions_manifest.json
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/manifest.json
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/reference/manifest.json
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/reference/models.json.gz
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/reference/reference.cdna.fa.gz
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/reference/reference.gtf.gz
examples/osteosarc_test_data/recipe/support/osteosarc/selection_validation/isovar/reference/reference.pep.fa.gz
examples/osteosarc_test_data/recipe/support/osteosarc/shared-v1/manifest.json
examples/osteosarc_test_data/recipe/support/report_expectations/additional_candidate_audit.json
examples/osteosarc_test_data/recipe/support/report_expectations/assembled_antigens.json
examples/osteosarc_test_data/recipe/support/report_expectations/assembled_rankings.json
examples/osteosarc_test_data/recipe/support/report_expectations/orf_platform_audit.json
examples/osteosarc_test_data/recipe/support/report_expectations/platform_comparison_audit.json
examples/osteosarc_test_data/recipe/support/report_expectations/sv_audits.json
vaxrank/__init__.py
vaxrank/allele_evidence.py
vaxrank/allele_validation.py
vaxrank/amino_acids.py
vaxrank/cancer_hotspots.py
vaxrank/candidate_epitope.py
vaxrank/cells.py
vaxrank/cleavage_inference.py
vaxrank/cleavage_profile.py
vaxrank/cleavage_report.py
vaxrank/combined_score_dsl.py
vaxrank/complex_variant_visualization.py
vaxrank/construct_audit.py
vaxrank/construct_sequence.py
vaxrank/context_audit.py
vaxrank/context_report.py
vaxrank/core_logic.py
vaxrank/coverage.py
vaxrank/cta_admission.py
vaxrank/download_test_data.py
vaxrank/epitope_config.py
vaxrank/epitope_dsl.py
vaxrank/epitope_io.py
vaxrank/epitope_logic.py
vaxrank/evidence_visualization.py
vaxrank/external_input.py
vaxrank/external_prediction.py
vaxrank/external_report.py
vaxrank/external_rescoring.py
vaxrank/gene_pathway_check.py
vaxrank/identifiers.py
vaxrank/isovar_fusion.py
vaxrank/junction_swap.py
vaxrank/logging.conf
vaxrank/manufacturability.py
vaxrank/manufacturability_config.py
vaxrank/modalities.py
vaxrank/mrna.py
vaxrank/mrna_library.py
vaxrank/mutant_protein_fragment.py
vaxrank/mutation_visualization.py
vaxrank/native_serialization.py
vaxrank/near_self.py
vaxrank/patient_info.py
vaxrank/peptide.py
vaxrank/prediction_input.py
vaxrank/processing.py
vaxrank/processing_prediction.py
vaxrank/ranking.py
vaxrank/reference_proteome.py
vaxrank/report.py
vaxrank/risk_ligand.py
vaxrank/safety_assessment.py
vaxrank/safety_policy.py
vaxrank/sequence_context.py
vaxrank/sid_test_data.py
vaxrank/tissue_risk.py
vaxrank/vaccine_antigen.py
vaxrank/vaccine_config.py
vaxrank/vaccine_library.py
vaxrank/vaccine_peptide.py
vaxrank/vaf.py
vaxrank/varcode_effects.py
vaxrank/vaxrank_results.py
vaxrank/version.py
vaxrank.egg-info/PKG-INFO
vaxrank.egg-info/SOURCES.txt
vaxrank.egg-info/dependency_links.txt
vaxrank.egg-info/entry_points.txt
vaxrank.egg-info/requires.txt
vaxrank.egg-info/top_level.txt
vaxrank/cli/__init__.py
vaxrank/cli/arg_parser.py
vaxrank/cli/complex_variant_visualization.py
vaxrank/cli/entry_point.py
vaxrank/cli/epitope_config_args.py
vaxrank/cli/evidence_visualization.py
vaxrank/cli/isovar_config_args.py
vaxrank/cli/mutation_visualization.py
vaxrank/cli/vaccine_config_args.py
vaxrank/config/__init__.py
vaxrank/config/default.yaml
vaxrank/config/defaults.py
vaxrank/config/loader.py
vaxrank/config/schema.py
vaxrank/data/cancer-driver-genes.csv
vaxrank/data/cancer-driver-variants.csv
vaxrank/data/cancer_hotspots_v2.tsv
vaxrank/data/class1-mhc-presentation-pathway.csv
vaxrank/data/interferon-gamma-response.csv
vaxrank/data/sid-test-data.zip
vaxrank/templates/cleavage_profiles.html
vaxrank/templates/construct_audit.html
vaxrank/templates/sequence_context_audit.html
vaxrank/templates/stylesheet.css
vaxrank/templates/template.html
vaxrank/templates/template.txt