Man pages for andrewrech/antigen.garnish
Ensemble neoepitope prediction from DNA variants in R

antigen.garnish'antigen.garnish': ensemble neoepitope prediction from DNA...
check_pred_toolsInternal function to check for netMHC tools, mhcflurry and...
collate_netMHCInternal function to collate results from netMHC prediction
detect_mhcReplace MHC with matching type in prediction tool format
extract_cDNAInternal function to extract cDNA changes from HGVS notation
garnish_jaffaProcess gene fusions and return a data table for neoepitope...
garnish_plotGraph 'garnish_predictions' results.
garnish_predictionsPerform neoepitope prediction.
garnish_summarySummarize neoepitope prediction.
garnish_variantsProcess VCF variants and return a data table for epitope...
get_metadataInternal function to add metadata by 'ensembl_transcript_id'
get_pred_commandsInternal function to create commands for neoepitope...
get_snpeffInternal function to extract SnpEff annotation information to...
get_ss_strParallelized function to create a space-separated character...
list_mhcList available MHC types using standard nomenclature
make_cDNAInternal function to create cDNA from HGVS notation
make_DAI_uuidInternal function to pair peptides from missense sites by a...
make_nmersInternal function for parallelized 'nmer' creation.
merge_predictionsInternal function to merge input data table and prediction...
run_mhcflurryInternal function to run run_mhcflurry commands.
run_mhcnuggetsInternal function to run run_mhcnuggets commands.
run_netMHCInternal function to run netMHC commands.
translate_cDNAInternal function to translate cDNA to peptides
write_mhcnuggets_nmersInternal function to output nmers for mhcnuggets prediction...
write_netmhc_nmersInternal function to output nmers for netMHC prediction to...
andrewrech/antigen.garnish documentation built on Oct. 8, 2017, 12:12 a.m.