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Would it be possible to add NetH2pan as a supported epitope prediction algorithm? NetH2pan is a standard benchmark/tool for MHC class I binding affinity predictions in mice.
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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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H2-Kb Y22F, M23I, E24S, D30N mutant
H2-d class I
H2-f class I
H2-b class I
H2-k class I
H2-r class I
H2-s class I
H2-z class I
H2-p class I
H2-q class I
H2-v class I
RT1-A
H2-Db Q70H mutan…
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Hi , I am using Hibag for HLA imputation. My dataset is GSA genotyped data.
I found when I use the function "hlaBED2Geno" to import the genotype data, there are around 8000 SNPS in the MHC region.…
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Hi,
I'm observing an apparent bug in which AnchorWave produces paf output with a CIGAR string that reports perfectly matching sequences as containing a matching insertion and deletion.
For examp…
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Related to mice. Right now we have HLA alleles from Ebi/Ensembl, but mice alleles have GenBank identifiers for names. We should rename them to something meaningful like H2-B, etc. This will also make …
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I'm trying to use very basic example of C++ API from tutorial:
ifstream ifs("mhc-opt.mol2");
ofstream ofs("mhc-opt.conv.pdb");
OpenBabel::OBConversion conv(&ifs, &ofs);
…
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**Mondo term (ID and Label)**
MONDO:0009455 immunodeficiency, partial combined, with absence of HLA Determinants and beta-2-microglobulin from lymphocytes
**Reason for deprecation**
OMIM 242870 i…
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I was able to run jtk successfully with the example reads, but I ran into an issue using my own nanopore reads.
Here is the tail of the output, running with `verbose = 2`
```
[2024-10-11T12:04…
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dear author:
i really like your tool, its precision and efficiency is definitly top around existing tools. recently i m trying to use SHAP https://github.com/shap/shap to test your model, but get ton…