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Hi,
I have 2 questions:
1- Is there a better documantion of the output files?
2- In the "neoantigens/sample1/Class_II/" diretory the following files are missing:
sample1_MHC_Class_I_all_epi…
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* pvactools version: 3.1.1
* Python version: 3.7 (from pVACtools docker hub image)
* Operating System: Debian 10 (from pVACtools docker hub image)
**Describe the bug**
When using NNAlign predict…
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Hi,
I am running the entire nextNEOpi pipeline on the TESLA dataset https://doi.org/10.1016/j.cell.2020.09.015 Currently, I'm experiencing issues with pVACsec for data from patient1, specifically som…
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can I select the neoantigen by the order of pvacseq output.
for example ,
Median MT Score； Median WT Score ；Median Fold Change
should I select by the Median Fold Change?
and the percentile rank i…
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Hi,
Thanks for developing a great tool!
I was wondering:
1. What is the motivation for focusing only on predicting binding affinity (and presentation) to MHC Class I and not Class II?
- Is…
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### Installation Type
Standalone
### pVACtools Version / Docker Image
4.0.0
### Python Version
3.9.1
### Operating System
CentOs 7
### Describe the bug
When I launch the following command I o…
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Hi,
After solving patch error (issue#14) by installing patch in our computation node, the pipeline run into a new error
```
Caused by:
Process `mixcr (Patient353_T1star : tumor_DNA)` termina…
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We have followed the procedure in: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf for evaluating potential neoantigens using no-enzyme.
PepQuery2 does not have option: -tag
Does …
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* pvactools version: 1.5.2
* Python version: 3.7.3
* Operating System: red hat 6
I ran pvacseq with NetMHCpan and NetMHCpanII. The combined filtered output (295 lines) has is less than the lines …
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Hi
I am wondering what is the best way to visualize the clones in a tree in order to accurately assess of the evolution or monoclonal or polyclonal.
I tried to check the stories Rdata and checked…