├── .gitignore ├── Example ├── HLAtypes │ └── hlatypes.txt └── input_vcfs │ ├── test1.vcf │ └── test2.vcf ├── LICENSE ├── NeoAlign.py ├── NeoClass.py ├── NeoPredPipe.py ├── NeoPredViz.md ├── NeoPredViz.py ├── NeoRecoPo.py ├── NeoRecoPoBlend.py ├── README.md ├── RecognitionPotential.md ├── StandardPredsClass.py ├── downstream_plotting.R ├── hla_preprocess.py ├── mart_table_hg38_unique.txt ├── ncbi_epitope_db └── IEDB_positive_T-cell_assays.fasta ├── neopredpipe_tests.py ├── netMHCpanAlleles.txt ├── netMHCpanAlleles2.txt ├── postprocessing.py ├── predict_binding.py ├── process_expression.py ├── test ├── Test_pepmatch.out ├── expression.txt ├── hla-II │ ├── Test_hlahd │ │ └── result │ │ │ └── Test_hlahd_final.result.txt │ ├── Test_hlaminer │ │ ├── HLAminer_HPRA.csv │ │ └── HLAminer_processed.txt │ └── hlatypes.txt ├── hlatypes.txt ├── hlatypes_multiallele.txt ├── hlatypes_strelka.txt ├── hlatypes_withIndels.txt └── vcfs │ ├── Test_multiAllele.vcf │ ├── Test_platypus.vcf │ ├── 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