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IEDB has now added support for running multiple version of some prediction algorithms. We should leverage that functionality. I suggest that we extend the list of prediction algorithms to have on item…
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The internal boundaries of netmhcpan regarding peptide lengths are 8 - 56. NetMHCpan 4.1 always picks the most relevant Core of the peptide and does prediction on it. That is currently prohibited by t…
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Currently, the pVACtools page lists support for four diff MHC Class II predication algorithms - NetMHCIIpan , SMMalign, NNalign and, MHCnuggets. The first three were added via IEDB, and MHCnuggets wa…
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```
p230198@peregrine:create_luts cat *.log
Rscript create_luts.R
Submitted batch job 13415020
Submitted batch job 13415021
Submitted batch job 13415023
#####################################…
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### Installation Type
Docker
### pVACtools Version / Docker Image
latest
### Python Version
_No response_
### Operating System
Ubuntu
### Describe the bug
When running pvacseq to make predict…
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Hello
thanks for devolving the neofox alogirhtem. I am trying to build a singularity container and then test the data sets. However, i can't figure out why the test data failed. Can you help to ch…
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Transformation of prediction score to its rank based on empirically approximated scoring distribution using random peptides of natural proteins
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Investigate adding support for this predictor that uses mass spec data to train unlike the other algorithms we currently support.
https://github.com/GfellerLab/MixMHCpred
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Greetings.
Looks like I have faced an issue that wasn't mentioned before.
Having downloaded your tool, I began with running an example with my vcf as an input (it can be downloaded below).
`
./t…
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Using `netmhccons` results in these errors, which come from `netmhc-3.4`:
```
Traceback (most recent call last):
File "/Users/julia/code/netmhc-bundle/netMHC-3.4/netMHC.py", line 535, in
…