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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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Dear Nick,
Thank you for the great package. After TCR annotation, how should we interpret the data. Here comes two typical output. I wanna categorize the antigen epitopes. For some of them (see f…
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This is a really great job and I have two questions for you:
1. When I use this model to make a prediction, I only have the TCR sequence that I need to predict and I don't know which epitopes to comb…
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Hi @riederd,
Thanks for your great end-to-end tool.
I encountered an installation problem using commands below:
`mamba env create -f assets/nextNEOpi.yml`
And the error message is like:
Wou…
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### Checklist
- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate
### What happened?
When I activate the conda environment or any environment created by th…
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Please update text definition: Restricting MHC role is a role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized \(bo…
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Hello
Thanks for your great tool.
I have a question about the input file. When I run epiTCR without MHC in prediction mode use pre-trained model. I find I must add the binder column. So is this …
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This is a great package, I am wondering whether we could predict the antigens or any other packages are recommended for antigen prediction?
Thank you very much!
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[tcrdist_alpha_sample.pdf](https://github.com/kmayerb/tcrdist3/files/13244328/tcrdist_alpha_sample.pdf)
Hi, tcrdist works fine when I use the sample data (dash.csv), but when I try it with other …
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Hi there,
If I read the code correctly then it seems that precision, recall & F1 are only computed on clustered data. Was that the intention? Like this it is possibe to come up with a "perfect" me…