├── LICENSE ├── README.md ├── aggregateSampleInfo.py ├── getNeoantigenBinders.sh ├── getNeoantigenBinders_KMAKallisto.sh ├── getPeptideList.py ├── kmaToPeptideSeqs.py ├── kma_output_file_example.csv ├── overallPipelineWrapper.sh ├── postprocessOutput.py ├── runNetMHCpan.py ├── run_kma_example.R ├── splitKMA.py └── splitKMA_KMAKallisto.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/README.md -------------------------------------------------------------------------------- /aggregateSampleInfo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/aggregateSampleInfo.py -------------------------------------------------------------------------------- /getNeoantigenBinders.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/getNeoantigenBinders.sh -------------------------------------------------------------------------------- /getNeoantigenBinders_KMAKallisto.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/getNeoantigenBinders_KMAKallisto.sh -------------------------------------------------------------------------------- /getPeptideList.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/getPeptideList.py -------------------------------------------------------------------------------- /kmaToPeptideSeqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/kmaToPeptideSeqs.py -------------------------------------------------------------------------------- /kma_output_file_example.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/kma_output_file_example.csv -------------------------------------------------------------------------------- /overallPipelineWrapper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/overallPipelineWrapper.sh -------------------------------------------------------------------------------- /postprocessOutput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/postprocessOutput.py -------------------------------------------------------------------------------- /runNetMHCpan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/runNetMHCpan.py -------------------------------------------------------------------------------- /run_kma_example.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/run_kma_example.R -------------------------------------------------------------------------------- /splitKMA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/splitKMA.py -------------------------------------------------------------------------------- /splitKMA_KMAKallisto.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vanallenlab/retained-intron-neoantigen-pipeline/HEAD/splitKMA_KMAKallisto.py --------------------------------------------------------------------------------