NEWS.md

In andrewrech/antigen.garnish: Tumor neoantigen prediction

antigen.garnish 2.3.1

Bugfix:

• errors parsing rare MHCII alleles for netMHC tools

antigen.garnish 2.3.0

Bugfix:

• update NetMHC tool data directory paths
• fix permissions on configuration script (was non-executable)
• minor documentation improvements

antigen.garnish 2.2.0

Bugfix:

• remove netMHC binary check from foreignness_score function that does not require netMHC binaries

antigen.garnish 2.1.0

Added functionality:

• add Dockerfile used to build publically available Docker image (andrewrech/antigen.garnish)
• relax parsing of SnpEff annotations to reduce errors across VCFs and/or SnpEff versions
• simplify internal functions that configure netMHC tools
• use Docker to run tests

antigen.garnish 2.0.0

Breaking changes:

• new filtering criteria based on TESLA: https://www.parkerici.org/research-project/tumor-neoantigen-selection-alliance-tesla/, see ?garnish_antigens
• update Ensembl transcript CDS database to release 101 (any prior versioned transcript release is acceptable)
• remove support for mitochondrial CDS, xlsx input, JAFFA input, PureCN input to focus on peptide/transcript tables and VCFs
• improve SnpEff annotation parsing

Additional updates:

• allow setting thread use via environment variable AG_THREADS
• include percentile rank filtering at default netMHC thresholds
• simplify installation instructions
• remove 7 dependencies
• additional integration tests
• do not export internal functions

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 dissimilarity_score
• 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
• dissimilarity_score dummy function present
• pulled most unnecessary mclapply loops to prevent parallelization failures
• functionalized foreignness_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

andrewrech/antigen.garnish documentation built on July 8, 2022, 5:19 p.m.