├── .github └── workflows │ └── tests.yml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASING.md ├── code-of-conduct.md ├── deploy.sh ├── develop.sh ├── docs ├── Makefile ├── conf.py └── index.rst ├── lint.sh ├── pylintrc ├── requirements.txt ├── run-vaxrank-b16-test-data.sh ├── setup.py ├── test.sh ├── tests ├── __init__.py ├── common.py ├── data │ └── b16.f10 │ │ ├── b16.combined.bam │ │ ├── b16.combined.bam.bai │ │ ├── b16.combined.sam │ │ ├── b16.combined.sorted.bam │ │ ├── b16.combined.sorted.bam.bai │ │ ├── b16.expressed.vcf │ │ ├── b16.f10.127a.aldh1b1.chr4.45802539.refG.altC.sam │ │ ├── b16.f10.127a.klf6.chr13.5864876.refC.altCG.sam │ │ ├── b16.f10.127a.phip.chr9.82927102.refG.altT.sam │ │ ├── b16.f10.127a.wdr13.chrX.8125624.refC.altA.sam │ │ ├── b16.f10.Phip.vcf │ │ ├── b16.f10.Wdr13.vcf │ │ ├── b16.not-expressed.vcf │ │ └── b16.vcf ├── test_cancer_driver_gene.py ├── test_epitope_prediction.py ├── test_manufacturability.py ├── test_mutant_protein_sequence.py ├── test_shell_script.py └── testing_helpers.py └── vaxrank ├── __init__.py ├── cli.py ├── core_logic.py ├── data ├── cancer-driver-genes.csv ├── cancer-driver-variants.csv ├── class1-mhc-presentation-pathway.csv └── interferon-gamma-response.csv ├── epitope_prediction.py ├── gene_pathway_check.py ├── logging.conf ├── manufacturability.py ├── mutant_protein_fragment.py ├── patient_info.py ├── reference_proteome.py ├── report.py ├── templates ├── stylesheet.css ├── template.html └── template.txt ├── vaccine_peptide.py └── vaxrank_results.py /.github/workflows/tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/vaxrank/HEAD/.github/workflows/tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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