LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
neofox/__init__.py
neofox/annotator.py
neofox/command_line.py
neofox/exceptions.py
neofox/neofox.py
neofox.egg-info/PKG-INFO
neofox.egg-info/SOURCES.txt
neofox.egg-info/dependency_links.txt
neofox.egg-info/entry_points.txt
neofox.egg-info/requires.txt
neofox.egg-info/top_level.txt
neofox/MHC_predictors/__init__.py
neofox/MHC_predictors/MixMHCpred/__init__.py
neofox/MHC_predictors/MixMHCpred/mixmhc2pred.py
neofox/MHC_predictors/MixMHCpred/mixmhcpred.py
neofox/MHC_predictors/netmhcpan/__init__.py
neofox/MHC_predictors/netmhcpan/abstract_netmhcpan_predictor.py
neofox/MHC_predictors/netmhcpan/combine_netmhcIIpan_pred_multiple_binders.py
neofox/MHC_predictors/netmhcpan/combine_netmhcpan_pred_multiple_binders.py
neofox/MHC_predictors/netmhcpan/netmhcIIpan_prediction.py
neofox/MHC_predictors/netmhcpan/netmhcpan_prediction.py
neofox/annotation_resources/__init__.py
neofox/annotation_resources/uniprot/__init__.py
neofox/annotation_resources/uniprot/uniprot.py
neofox/expression_imputation/__init__.py
neofox/expression_imputation/expression_imputation.py
neofox/expression_imputation/tcga_cohort_code.tab
neofox/expression_imputation/tcga_exp_summary_modified.tab.gz
neofox/expression_imputation/tcga_exp_summary_modified.tab.gz.tbi
neofox/helpers/__init__.py
neofox/helpers/blastp_runner.py
neofox/helpers/epitope_helper.py
neofox/helpers/intermediate_files.py
neofox/helpers/runner.py
neofox/model/__init__.py
neofox/model/conversion.py
neofox/model/mhc_parser.py
neofox/model/neoantigen.py
neofox/model/validation.py
neofox/model/wrappers.py
neofox/published_features/__init__.py
neofox/published_features/expression.py
neofox/published_features/prime.py
neofox/published_features/priority_score.py
neofox/published_features/Tcell_predictor/Classifier.pickle
neofox/published_features/Tcell_predictor/SIRdata.mat
neofox/published_features/Tcell_predictor/__init__.py
neofox/published_features/Tcell_predictor/amino-acids-features.pickle
neofox/published_features/Tcell_predictor/genes-expression.pickle
neofox/published_features/Tcell_predictor/preprocess.py
neofox/published_features/Tcell_predictor/tcellpredictor_wrapper.py
neofox/published_features/differential_binding/__init__.py
neofox/published_features/differential_binding/amplitude.py
neofox/published_features/differential_binding/differential_binding.py
neofox/published_features/dissimilarity_garnish/__init__.py
neofox/published_features/dissimilarity_garnish/dissimilaritycalculator.py
neofox/published_features/hex/BLOSUM62.rda
neofox/published_features/hex/EPItOMe_modified.R
neofox/published_features/hex/__init__.py
neofox/published_features/hex/hex.R
neofox/published_features/hex/hex.py
neofox/published_features/iedb_immunogenicity/__init__.py
neofox/published_features/iedb_immunogenicity/iedb.py
neofox/published_features/neoag/__init__.py
neofox/published_features/neoag/neoag_gbm_model.py
neofox/published_features/neoag/neoag-master/Final_gbm_model.rds
neofox/published_features/neoag/neoag-master/LICENSE.txt
neofox/published_features/neoag/neoag-master/NeoAg_immunogenicity_predicition_GBM.R
neofox/published_features/neoantigen_fitness/__init__.py
neofox/published_features/neoantigen_fitness/neoantigen_fitness.py
neofox/published_features/self_similarity/BLOSUM62-2.matrix.txt
neofox/published_features/self_similarity/__init__.py
neofox/published_features/self_similarity/self_similarity.py
neofox/published_features/vaxrank/__init__.py
neofox/published_features/vaxrank/vaxrank.py
neofox/references/__init__.py
neofox/references/install_r_dependencies.R
neofox/references/installer.py
neofox/references/references.py
neofox/tests/__init__.py
neofox/tests/fake_classes.py
neofox/tests/integration_tests/__init__.py
neofox/tests/integration_tests/integration_test_tools.py
neofox/tests/integration_tests/test_alternative_mutation.py
neofox/tests/integration_tests/test_best_multiple_binder.py
neofox/tests/integration_tests/test_blast.py
neofox/tests/integration_tests/test_dissimilarity.py
neofox/tests/integration_tests/test_hex.py
neofox/tests/integration_tests/test_mixmhcpred.py
neofox/tests/integration_tests/test_neoag.py
neofox/tests/integration_tests/test_neoantigen_fitness.py
neofox/tests/integration_tests/test_neofox.py
neofox/tests/integration_tests/test_netmhcpan.py
neofox/tests/integration_tests/test_prime.py
neofox/tests/synthetic_data/__init__.py
neofox/tests/synthetic_data/data_generator.py
neofox/tests/synthetic_data/factories.py
neofox/tests/synthetic_data/test_synthetic_data.py
neofox/tests/unit_tests/__init__.py
neofox/tests/unit_tests/test_dependencies_configuration.py
neofox/tests/unit_tests/test_differential_binding.py
neofox/tests/unit_tests/test_epitope_helper.py
neofox/tests/unit_tests/test_expression.py
neofox/tests/unit_tests/test_expression_annotation.py
neofox/tests/unit_tests/test_hla_database.py
neofox/tests/unit_tests/test_iedb_immunogenicity.py
neofox/tests/unit_tests/test_mhc_parser.py
neofox/tests/unit_tests/test_models.py
neofox/tests/unit_tests/test_neofox.py
neofox/tests/unit_tests/test_priority_score.py
neofox/tests/unit_tests/test_reference_folder.py
neofox/tests/unit_tests/test_runner.py
neofox/tests/unit_tests/test_self_similarity.py
neofox/tests/unit_tests/test_synthetic_data.py
neofox/tests/unit_tests/test_tcell_predictor.py
neofox/tests/unit_tests/test_uniprot.py
neofox/tests/unit_tests/test_validation.py
neofox/tests/unit_tests/test_wrappers.py
neofox/tests/unit_tests/tools.py