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Hello,
we have generated an HLA-peptides library using PeptDeep-HLA for the prediction of peptides and alphapeptdeep for library generation and conversion to .tsv for compatibility with DIANN. Then…
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Hello.
Thanks for this amazing work.
I tried to run the example scripts but I got
```
(HYDRA) :~/softwares/HYDRA$ python3 scripts/sample-pdb.py data/pfemp1/PF3D71150400_MEDIUM.pdb configs/train.ym…
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Is there a way to specify the minimum or maximum peptide length for a search? I noticed that the default value for minimum peptide length is 6 from the output .pglyco file but couldn't find a way to m…
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Hi,
i used a peptide database build by myself to generate a spectral library, however, i found that when i used the library to search, the outcome file is only 1kb with empty information. and i…
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**Steps to Reproduce**
**Case 1**
1. Add some molecules and structures on canvas in micro mode ( e.g. Benzene ring, molecules )
2. Switch to Macro mode and hover over abbreviations
**Case 2**
1…
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Dear colleagues,
It would be very helpful to have example files to work with progenesis.
Particularly the peptides file (does it have to be .txt?) and annotation file.
Àlex Bayés
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Currently this code works for peptides in 12 -24 AA range. it appears this in enforced for the percentile calculation. Would removing this limitation still allow for the log odd calcualtions?
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@dfermin:
I'm doing some analysis here and I found that when `decoys` are not exported some of the peptides in the input are not exported, but when the `decoys` are exported, then they appear.
…
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So far rawDiag supports:
- iRT (Biognosys)
- 6 x 5 LC-MS/MS Peptide Ref. Mix (Promega)
- MSQC1 (Sigma)
Are there other peptide sets that could make sense?
**PROCAL**
Zolg, D. P., Wilhelm, …
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Hello,
My understanding is that the `coord` column contains the coordinates of the _splicing event_ (e.g. the coordinates may be that of a skipped exon) and not the genomic coordinates of the seque…