antigen.garnish 1.1.1

  • update to include configuration for netMHC dependencies
  • support for paired wild-type and mutant protein level input

antigen.garnish 1.1.0

  • added garnish_dissimilarity
  • updated readme citation, link to manuscript repository
  • externalized smith-waterman alignment function
  • appropriate test updates
  • remove deprecated garnish_fitness function
  • update to LICENSE

antigen.garnish 1.0.0

  • prepare for the release of the antigen.garnish manuscript
  • multiple metrics of antigen quality are now computed
  • garnish_dissimilarity dummy function present
  • pulled most unnecessary mclapply loops to prevent parallelization failures
  • functionalized iedb_score code into external function
  • garnish_plot, garnish_summary now incorporate antigen quality metrics
  • garnish_antigens now returns ranked antigens by quality metrics
  • numerous edge case, efficiency updates and bug fixes

antigen.garnish 0.0.6

  • clonality filter added to garnish_affinity
  • RNA expression filter added to garnish_affinity
  • fitness model implemented in R vs. Python
  • garnish_antigens function added to rank neoantigens
  • garnish_score function added to return sample level immune fitness summary
  • updated summary and plot functions with better output
  • added wiki with installation instructions
  • numerous edge case bug fixes
  • remove biomaRt dependencies

antigen.garnish 0.0.5

  • add ncbi-blast functionality to determine neoantigen near matches
  • add ncbi-blast functionality to determine known IEDB matches
  • implement antigen fitness model of Lukza et al. Nature 2017

antigen.garnish 0.0.4

  • add summary plots
  • improve test coverage

antigen.garnish 0.0.3

  • inverse match against global normal proteins
  • improve testing, test formatting

antigen.garnish 0.0.2

  • add prediction deduplication to garnish_affinity
  • add gene fusions as a source of neoantigens using garnish_jaffa
  • stable API

antigen.garnish 0.0.1

  • initial version