Neoantigen prediction

Predict neoantigen affinity using antigen.garnish.

antigen.garnish

antigen.garnish: ensemble neoantigen prediction from DNA variants in R.

garnish_variants()

Process VCF variants and return a data table for epitope prediction.

garnish_jaffa()

Process gene fusions and return a data table for neoantigen prediction.

garnish_affinity()

Perform neoantigen prediction.

Summarize and visualize results

Summarize and visualize filtered ensemble neoantigen prediction results.

garnish_summary()

Summarize neoantigen prediction.

garnish_antigens()

List top neoantigens for each sample and/or by clones within each sample.

garnish_plot()

Graph garnish_affinity results.

garnish_slim()

Return minimal neoantigen prediction information for all peptides.

Helpers

Helper functions for using the antigen.garnish package.

check_dep_versions()

Internal function to check for dev version of magrittr.

check_pred_tools()

Internal function to check for netMHC tools, mhcflurry and mhcnuggets

collate_netMHC()

Internal function to collate results from netMHC prediction

detect_mhc()

Internal function to replace MHC with matching prediction tool MHC syntax

extract_cDNA()

Internal function to extract cDNA changes from HGVS notation

garnish_clonality()

Internal function to integrate clonality data into output.

garnish_dissimilarity()

Return dissimilarity (to reference proteome) values for a vector of nmers.

get_metadata()

Internal function to add metadata by ensembl_transcript_id

get_pred_commands()

Internal function to create commands for neoantigen prediction.

get_ss_str()

Parallelized function to create a space-separated character string between two integers

get_vcf_info_dt()

Internal function to extract a data table of variants with INFO fields in columns.

get_vcf_sample_dt()

Internal function to extract a data table from sample vcf fields.

get_vcf_snpeff_dt()

Internal function to extract SnpEff annotation information to a data table.

iedb_score()

Return iedb_scores for a vector of nmers.

list_mhc()

Return a data table of available MHC types.

make_BLAST_uuid()

Internal function to categorize mutant and wild-type peptides by similarity using BLAST to calculate neoantigen amplitude and homology to IEDB antigens.

make_DAI_uuid()

Internal function to pair peptides from missense sites by a common UUID for DAI calculations

make_cDNA()

Internal function to create cDNA from HGVS notation

make_nmers()

Internal function for parallelized nmer creation.

merge_predictions()

Internal function to merge input data table and prediction results

run_mhcflurry()

Internal function to run run_mhcflurry commands.

run_mhcnuggets()

Internal function to run run_mhcnuggets commands.

run_netMHC()

Internal function to run netMHC commands.

translate_cDNA()

Internal function to translate cDNA to peptides

write_mhcnuggets_nmers()

Internal function to output nmers for mhcnuggets prediction to disk

write_netmhc_nmers()

Internal function to output nmers for netMHC prediction to disk