immune-health/antigen.garnish: Ensemble tumor neoantigen prediction and multi-parameter quality analysis from direct input, SNVs, indels, or gene fusion variants

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.

Getting started

Package details

Maintainer
LicenseSee LICENSE
Version1.1.1
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("immune-health/antigen.garnish")
immune-health/antigen.garnish documentation built on Dec. 30, 2019, 11:54 p.m.