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I'm trying to use NetMHCIIpan to predict epitope binding to a mouse class II allele, H2-IEd. Output of `pvacseq valid_algorithms -a H2-IEd` suggests that it is not supported by NetMHCIIpan, yet it is …
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I'm trying to install netMHCpan and netMHCIIpan but I'm with difficulties. In the terminal shows these output
1 protein sequences
/bin/sh: 1: netMHCpan: not found
netmhcpan not installed
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Class II predictions have a lot of redundancy in the peptides they spit out which can be reduced by looking at the Core sequence. Currently topiary doesn't output the Core of a peptide (to match the …
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### Description of the bug
The epaa.py script expects a `--reference_proteome` as argument, however via the nextflow script only `--proteome` is parsed:
https://github.com/nf-core/epitopepredictio…
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The current [output parser for NetMHCpan4](https://github.com/openvax/mhctools/blob/master/mhctools/parsing.py#L359-L401) is no longer compatible with the output of NetMHCpan-4.1.
Also similar for …
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Having a look at [this repository](https://github.com/kevinkovalchik/PyNetMHCpan) which is:
> A simple tool for using NetMHCpan and NetMHCIIpan using multiple CPUs in a Python environment.
- is it…
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when request data from NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan, the program may stop of request error, but can recue when rerun, so is it convenient for you to add retry functions like https://github.…
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Expected Behavior:
All PDBs in the template set has allele assigned, especially for anchor prediction using NetMHCIIpan
Current Behavior:
Some PDBs e.g. 6XP6, 7KEI still do not have allele assign…
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6 April 2020 09:44 3 KB
From:
Richel Bilderbeek
To: Morten Nielsen
Dear Mr. Nielsen,
Thanks for writing NetMHC2pan! I've (contacted and) thanked you earlier, but again: thanks for your work!
…
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Error received:
```
Traceback (most recent call last):
File "/Users/Ryan/anaconda2/bin/topiary", line 64, in
main()
File "/Users/Ryan/anaconda2/bin/topiary", line 46, in main
epitopes = …