├── LICENSE ├── README.md ├── add_path.sh ├── configureArgs ├── configureArgs.bk ├── data ├── ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz ├── ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz.tbi ├── iedb.fasta └── iedb │ ├── iedb.fasta.phd │ ├── iedb.fasta.phi │ ├── iedb.fasta.phr │ ├── iedb.fasta.pin │ ├── iedb.fasta.pog │ ├── iedb.fasta.psd │ ├── iedb.fasta.psi │ └── iedb.fasta.psq ├── delete-normal-samplesFromVCF.sh ├── python ├── Aligner.py ├── Aligner.pyc ├── Neoantigen.py ├── Neoantigen.pyc └── main.py ├── r └── generate_input_of_NQcomputation.R ├── runNEO ├── runNEO_prepare ├── runNEO_run ├── step1-transformMaf2VCF.sh ├── step2-NEOcomputation_parallel.sh ├── step2-NEOcomputation_serial.sh ├── step3-neoantigenQcomputation.sh ├── step3-summaryNeoantigens.sh └── test ├── input.maf └── input_HLA.tsv /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/README.md -------------------------------------------------------------------------------- /add_path.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/add_path.sh -------------------------------------------------------------------------------- /configureArgs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/configureArgs -------------------------------------------------------------------------------- /configureArgs.bk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/configureArgs.bk -------------------------------------------------------------------------------- /data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz -------------------------------------------------------------------------------- /data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz.tbi -------------------------------------------------------------------------------- /data/iedb.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb.fasta -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.phd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.phd -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.phi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.phi -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.phr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.phr -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.pin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.pin -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.pog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.pog -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.psd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.psd -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.psi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.psi -------------------------------------------------------------------------------- /data/iedb/iedb.fasta.psq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/data/iedb/iedb.fasta.psq -------------------------------------------------------------------------------- /delete-normal-samplesFromVCF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/delete-normal-samplesFromVCF.sh -------------------------------------------------------------------------------- /python/Aligner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/python/Aligner.py -------------------------------------------------------------------------------- /python/Aligner.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/python/Aligner.pyc -------------------------------------------------------------------------------- /python/Neoantigen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/python/Neoantigen.py -------------------------------------------------------------------------------- /python/Neoantigen.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/python/Neoantigen.pyc -------------------------------------------------------------------------------- /python/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/python/main.py -------------------------------------------------------------------------------- /r/generate_input_of_NQcomputation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/r/generate_input_of_NQcomputation.R -------------------------------------------------------------------------------- /runNEO: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/runNEO -------------------------------------------------------------------------------- /runNEO_prepare: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/runNEO_prepare -------------------------------------------------------------------------------- /runNEO_run: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/runNEO_run -------------------------------------------------------------------------------- /step1-transformMaf2VCF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/step1-transformMaf2VCF.sh -------------------------------------------------------------------------------- /step2-NEOcomputation_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/step2-NEOcomputation_parallel.sh -------------------------------------------------------------------------------- /step2-NEOcomputation_serial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/step2-NEOcomputation_serial.sh -------------------------------------------------------------------------------- /step3-neoantigenQcomputation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/step3-neoantigenQcomputation.sh -------------------------------------------------------------------------------- /step3-summaryNeoantigens.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/step3-summaryNeoantigens.sh -------------------------------------------------------------------------------- /test/input.maf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/test/input.maf -------------------------------------------------------------------------------- /test/input_HLA.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShixiangWang/Variants2Neoantigen/HEAD/test/input_HLA.tsv --------------------------------------------------------------------------------