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Mutant peptide ranking for personalized cancer vaccines

Project description

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Selection of mutated protein fragments for therapeutic personalized cancer vaccines.


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


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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