antigen.garnish 2.3.1

antigen.garnish 2.3.1

docker pull andrewrech/antigen.garnish:2.3.1

Bugfixes:

• errors parsing rare MHCII alleles for netMHC tools
• update NetMHC tool data directory paths
• fix permissions on configuration script (was non-executable)
• minor documentation improvements
• remove netMHC binary check from foreignness_score function that does not require netMHC binaries

antigen.garnish 2.1.1

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, 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:

• include percentile rank filtering at default netMHC thresholds
• simplify installation instructions
• remove 7 dependencies
• additional integration tests
• do not export internal functions

antigen.garnish version 1.1.1

Updates since last release:

• paired wild-type and mutant peptide input
• update to include support for all netMHC versions

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

• 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

0.0.5

Jenkins

0.0.4

0.4.0