├── .github └── workflows │ └── tests.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── RELEASING.md ├── deploy.sh ├── develop.sh ├── lint.sh ├── pylintrc ├── requirements.txt ├── setup.py ├── test.sh ├── test ├── __init__.py ├── data.py ├── data │ ├── B16-StringTie-chr1-subset.gtf │ ├── genes.fpkm_tracking │ ├── isoforms.fpkm_tracking │ └── tiny_test_ligandome_dir │ │ ├── A0201 │ │ └── HLA-B0704 ├── test_args_outputs.py ├── test_cli_protein_changes.py ├── test_contains_mutant_residues.py ├── test_dataframe.py ├── test_effect_expression_filters.py ├── test_epitopes_from_commandline_args.py ├── test_load_cufflinks_fpkm.py ├── test_load_stringtie_gtf_fpkm.py ├── test_mutant_epitope_predictions_class1.py ├── test_mutant_epitope_predictions_class2.py ├── test_padding.py ├── test_peptide_mutation_interval.py ├── test_rna_helpers.py └── test_variant_expression_filters.py └── topiary ├── __init__.py ├── cli ├── __init__.py ├── args.py ├── errors.py ├── filtering.py ├── outputs.py ├── protein_changes.py ├── rna.py ├── script.py └── sequence.py ├── filters.py ├── predictor.py ├── rna ├── __init__.py ├── common.py ├── cufflinks.py └── gtf.py └── sequence_helpers.py /.github/workflows/tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/topiary/HEAD/.github/workflows/tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/topiary/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/topiary/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: 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