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Hello,
Is there any plans to implement this workflow https://github.com/griffithlab/anchor_huiming_etal_2023 in pvacseq, described in the https://www.science.org/doi/full/10.1126/sciimmunol.abg2200…
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### Installation Type
Docker
### pVACtools Version / Docker Image
griffithlab/pvactools:4.0.1
### Python Version
_No response_
### Operating System
_No response_
### Describe the bug
Encouter…
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Hi,
I was wondering if there is a way to run the nextNEOpi pipeline just from the pVACseq command? I want to run it first with standard and then relaxed filtering. I changed the setting in params.c…
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I am running neo (v1.0.1), and get the following warning: Linx neo-epitope file(tumor-id.linx.neoepitope.tsv) not found.
The neo-epitope file generated from Linx (v1.23.6) is named tumor-id.linx.…
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I am trying to find how the neoepitope files (*.isf.neoepitope.csv) from isofox are created. In particular, I want to understand the method used to predict neoepitope counts.
I have looked through …
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**Describe the bug**
The snappy step dependencies in cubi-tk/snappy/common do currently not fully match the state of snappy. This means that i.e. `cubi-tk snappy kickoff`will not start certain steps,…
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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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Right now, for each variant, we select the best peptide like so:
Sort all entries in the all_epitopes file for the variant by lowest MT IC50, lowest TSL, and highest WT IC50. Then select the first en…
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# 生信爱好者周刊（第 74 期）：
这里记录每周值得分享的生信相关内容，周日发布。
本杂志开源（GitHub: [ShixiangWang/weekly](https://github.com/ShixiangWang/weekly)），欢迎提交 issue，投稿或推荐生信相关内容。
[「生信周刊讨论区」](https://github.com/ShixiangWang/wee…
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I keep getting a
```
Traceback (most recent call last):
File "/Users/naqvia/Desktop/yes/envs/JCAST/bin/jcast", line 8, in
sys.exit(main())
File "/Users/naqvia/Desktop/yes/envs/JCAST/l…