Predict cancer epitopes from cancer sequence data
Project description
Predict mutation-derived cancer T-cell epitopes from (1) somatic variants (2) tumor RNA expression data, and (3) patient HLA type.
Example
/topiary
--vcf somatic.vcf
--mhc-pan
--mhc-alleles HLA-A*02:01,HLA-B*07:02
--ic50-cutoff 500
--percentile-cutoff 2.0
--mhc-epitope-lengths 8-11
--rna-gene-fpkm-file genes.fpkm_tracking
--rna-min-gene-expression 4.0
--rna-transcript-fpkm-file isoforms.fpkm_tracking
--rna-min-transcript-expression 1.5
--output-csv epitopes.csv
--output-html epitopes.html
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