antigen.garnish
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andrewrech
Hi, I have a question regarding the dai_uuid column as I want to compare the mutated peptides with their wt peptide. I was told that this is the column to...
Hi, I have been trying to run antigen garnish for a while with your testdata and now it seems to run fine with parallel and netMHC. The issue is that...
Hi, So I have attached my output for the function "garnish_antigens" with the default parameters set in the user manual. I was trying to understand the meaning of all the...
v %>% foreignness_score(db = "human") %>% print Removing temporary fasta files. nmer 1: SIINFEKL 2: ILAKFLHWL 3: GILGFVFTL Warning message: In foreignness_score(., db = "human") : Skipping BLAST because ncbiblast+...
Hi, I have been attempting to explore some MHCII alleles for Balb-c mice. I read in the file below with fread (from data.table) and ran garnish affinity on the data...
Hi, I am attempting to use antigen garnish to predict neoantigens from fusion proteins predicted by arriba/starfusion/fusioncatcher. I took the predicted peptides from those programs (quite long, minimum of 60...
Hi, We are trying to run antigen garnish on a GATK generated vcf. We get the error below when calling garnish_variants(file). Any insights? All variants processed Error in stri_replace_all_regex(string, pattern,...
Hi, Just wanted to check before I got too in depth into the download for this, does the foreignness calculation have compatibility with mice?
Hi, I have followed the instructions to install the software via Docker, but but I am not able to load the rio package to use the tool with annotated VCF...
Hi Andrew, I just started using antigen.garnish for a VCF file I have, but it reported the error below that I cannot overcome. `> garnish_variants("test.vcf") Loading VCFs Scanning file to...
