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a slightly annoying problems is that the neoantigen candidates file and the Peptide 51mer are not in the same order, which results in a slight inconvenience when manually reviewing. @malachig and I h…
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Hello there, I would like to seek clarification for these columns in the filtered.tsv output file:
1. Start / Stop column: Does "start" correspond to the genomic coordinates of the 5' partner of th…
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Dear author,
Thank you for the nice pipeline. I recently ran nextNEOpi pipeline on one sample( DNA tumor, DNA normal and RNA tumor).
The pipeline produced all expected five folders. However, in a…
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Hello I am trying to run the example with this user_ini.path
```
[annovar]
convert2annovar = /home/davide.rambaldi/src/annovar/convert2annovar.pl
annotatevariation = /home/davide.rambaldi/src/an…
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Hi, I wanted to express my appreciation for your exceptional work in developing the impressive tool NeoPredPipe. I have a question regarding its functionality: What is the source of the expression col…
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Dear Developers
Your tool is very great. Today I have a new question. I'm using the wrapper tool to model multiple peptides at the same time. The peptides are reported in datafile.tsv and for each …
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I am very interested in these standards listed in the file fda_quality_thresholds.csv. However, I have been unable to locate a specific source or reference for these standards. Were these standards de…
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Hi there,
Firstly, I ran `GenerateScores.py` with below commands:
```
python ../src/GenerateScores.py ../examples/nmer_test_input.xlsx HLA-A02:01 HLA-A03:01 HLA-B13:02 HLA-B15:01 HLA-C05:01 HLA-C…
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Hello developer!
Thank you for the wonderful tool you put together.
I got an error which I don't know where it come from. Running test worked fine, but when I use the real data it results in this …
ghost updated
11 months ago
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Dear developers of Pandora
Do you have any tips about modeling MHC-I 9mers of mut/wt peptides derived from Single nucleotide variants?
I have the following case of study
mut peptide:CVRVSGQ…