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* pvactools version: 1.5.4
my pvactools version is 1.5.4 , and I found in the article that NetMHCpan 4.0 predict peptides to any MHC molecule 。 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC67144…
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Original issue: https://github.com/griffithlab/pVAC-Seq/issues/222
Take the peptide sequence and do some sort of similarity search against the ref proteome (BLAST) to see if the peptide naturally e…
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Would be great if we can annotate this list:
```
PXD004732 -- ProteomeTools -- 104608
PXD000561 -- A draft map of the human proteome -- 97948
PXD002815 -- A human interactome in three quantitat…
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* pvactools version: 1.5.3
* Python version: 2.7
* Operating System: ?
Using docker(griffithlab/pvactools:1.5.3) within MGI cluster research-hpc
**Describe the bug**
pVACfuse does not recognize…
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@davidballi might be better to work in [clonality branch](https://github.com/andrewrech/antigen.garnish/tree/clone_wars), as there are new columns. think it is going to take us a while to merge this.
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Hi,
I am planning on using immunonode's neoepitope script for [mhcquant](https://github.com/nf-core/mhcquant). However, the currently implemented epitope prediction tools don't support enough lengt…
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```
root@a231da4504f2:~/notebooks/neoepiscope# neoepiscope call -x ~/neoepiscope.data/hg19 -d ~/neoepiscope.data/gencode_v29/ -c adjusted_hap_som_germ.out -a HLA-A -o tests/output_prediction_somatic_…
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pvactools version: 1.3.0
Python version: 3.5.5
Operating System: Linux
**Describe the bug**
`.filtered` file is empty even though there are plausible candidates in `.all_epitopes` file
**To R…
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When run the "Predict neoepitopes" example, I get this:
> Meta line 56 read in.
> All meta lines processed.
> Character matrix gt created.
> Character matrix gt rows: 3
> Character matrix gt co…
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Hi,
I have a problem about inputfile.
I have vep.vcf file that include chromosome position with "chr".
but my readcount file have not "chr" letter, DNA(normal,tumor),RNA all of them.
so, I alt…