Examples

Demo dataset

Sample input:

• Neoantigens input file

• Patients input file

Command:

neofox --input-file test_data.tsv --patient-data test_patients.tsv --output-folder your_folder --output-prefix test --with-all-neoepitopes --organism human

Sample output:

• Annotated neoantigens in tabular format

• Annotated neoantigens and neoepitopes in JSON format

• Annotated MHC-I neoepitopes in tabular format

• Annotated MHC-II neoepitopes in tabular format