antigen.garnish: ensemble neoantigen prediction from DNA variants in R. — antigen.garnish" />

An R package for neoantigen analysis that takes human or murine DNA missense mutations, insertions, deletions, or RNASeq-derived gene fusions and performs ensemble neoantigen prediction using 7 algorithms. Input is a VCF file, JAFFA output, or table of peptides or transcripts. Outputs are ranked and summarized by sample. Neoantigens are ranked by MHC I/II binding affinity, clonality, RNA expression, similarity to known immunogenic antigens, and dissimilarity to the normal peptidome.

Details

Advantages

  1. Thoroughness:

  • missense mutations, insertions, deletions, and gene fusions

  • human and mouse

  • ensemble MHC class I/II binding prediction using mhcflurry, mhcnuggets, netMHC, netMHCII, netMHCpan and netMHCIIpan

  • ranked by

    • MHC I/II binding affinity

    • clonality

    • RNA expression

    • similarity to known immunogenic antigens

    • dissimilarity to the normal peptidome

  1. Speed and simplicity:

  1. Integration with R/Bioconductor

  • upstream/VCF processing

  • exploratory data analysis, visualization

Package documentation (pdf)

We welcome contributions and feedback via Github or email.

See also