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Hi,
thanks for the code. How can I generate only peptides (smaller proteins) using transfer learning, can I finetune (valid_data) on peptides or is there some tweak etc? thanks!
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I encountered an error while using this method: KeyError: 'XcXgXyXtXyXgXd'. So, I checked the result returned by the get_struc_seq method. The seq, which should store the original amino acid sequence,…
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The alphafold models can run using swiftTCR but the only problem is that it tries to connect the peptide to the MHC when viewed in PyMol. This is because of this line
`command = "pdb_tidy {} | pdb_…
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Hi all,
I'm currently processing an LFQ-DiaNN output using the iq package. My code below works fine except that the peptide_extractor worked once but then stopped working the next day. Any ideas wh…
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Currently, pVACseq does not prefilter transcripts on their biotype. We prioritize protein_coding transcripts when picking the best peptide and transcript in the aggregate report creation.
In pVACsp…
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Hi @YichengLin-lab,
While I am studying your research team's paper and trying to run code with the following command:
**python main.py --peptide VMMGLLMFS --HLA HLA-A*26:01 --num_simulations 10** …
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e.g. it would be nice to have Infos like mass and charge in there as well
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Hi Vadim and team,
I have done 3 plex dimethyl labeling on samples and am now trying to analyze them following the steps outlined in the plexDIA section. But as you can see below, after finished wi…
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Hello,
Thank you for developing DIA-NN.
I am new to DIA-NN and mass spec in general. I am currently trying to use DIA-NN to extract fragment level data and have successfully managed to run it t…
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```
In the current specification it's stated (page 26): "The protein's accession
the peptide is associated with. In case no protein section is present in the
file or the peptide was not assigned to …