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Thank you for sharing this nice toolkit of neoantigen identification!
I have finished the T antigen workflow analyses while some errors occurred in the Interactive Neoantigen Viewer. The table of …
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I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptide…
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There are many neoantigen tools and pipelines out there.
Let's investigate these tools and consider adding them so ours can be the best!
Add all tools/pipelines of interest to the document here:…
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Hi,
I have been testing pVAC-seq with a few samples. For each sample, I have typically 150-400 somatic PASS mutations, of which ~40-75 are missense variants. I am using quite a new version of pVACt…
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Hi,
Can you please teach us a bit about how to navigate through the resulting output? I am aware that each column is reporting a different aspect of an immunological assessment, but is there an eas…
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Hi
I am trying to do fusion neoantigen prediction using Arriba, however STAR can't cope with long reads and ideally STARlong should be used - do you think this will be able to be supported please?
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Hi,
Does you tool work with mm10 (mouse) data? As far as I know, NetMHCpan-4.0 permitts to work with it, but I did not find this possibility in your documentation.
Thanks
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A neoantigen prediction pipeline from [Hammerlab](https://github.com/hammerlab/epidisco), mostly making use of the [Isovar](https://github.com/openvax/isovar) tool from OpenVax.
This seems to be on…
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https://github.com/griffithlab/pVACtools/blob/7c4b383c554a62352c74a92884bc5214267810b1/pvactools/tools/pvacseq/generate_protein_fasta.py#L45C1-L48C6
The `generate_protein_fasta.py` script uses the …
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