Mutant peptide ranking for personalized cancer vaccines
Project description
vaxrank
Selection of mutated protein fragments for therapeutic personalized cancer vaccines.
Usage
vaxrank \
--vcf test/data/b16.f10/b16.vcf \
--bam test/data/b16.f10/b16.combined.bam \
--vaccine-peptide-length 25 \
--mhc-predictor netmhc \
--mhc-alleles H2-Kb,H2-Db \
--padding-around-mutation 5 \
--output-ascii-report vaccine-peptides.txt \
--output-pdf-report vaccine-peptides.pdf \
--output-html-report vaccine-peptides.html
Installation
Vaxrank can be installed using pip:
pip install vaxrank
Note: to generate PDF reports, you first need to install wkhtmltopdf, which you can do (on OS X) like so:
brew install Caskroom/cask/wkhtmltopdf
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