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Hello,
First of all, I would like to commend you on the excellent work you have done with O-Pair. It is an incredibly powerful tool for O-glycopeptide identification, and it has significantly enhan…
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Hello DeepNeuropePred Team,
First of all, I would like to thank you for developing the DeepNeuropePred tool and making it available to the community. It's a valuable resource for researchers intere…
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Hello,When I used signalP 6.0 to predict signal peptides, I found that there are negative values for Cleavage sites in the output.gff3 file. What is the reason?
Example:
"RS_3_bin.18_00081 hypothe…
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Hello,
I was applying your pipeline to some sc-data from the allen brain atlas and i got a handful of negative values for the 3'UTR length in my sce object. I was using the utrome_mm10_v2. One exam…
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I noticed that there are some other SO term annotated that have residues. Should any of these feature be included in the feature viewer? (Show details to see the residues)
- https://www.pombase…
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We want some filtering capabilities for peptide characteristics.
From Rui:
- Peptides identified in DIA data
- Filter out those peptides that contain Cysteine
- Filter out those peptides that co…
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I thought it might be useful to have a separate thread to discuss metabolism.
The program I used predicts the potential sites of metabolism but does not predict rates so I can't say with any reliabil…
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Hey,
I saw that the decoy generation is done by Comet. Parameter `decoy_search = 1`. I think, but correct me, Comet is using reverse decoys? Which is of course greate for reproducablitly, especiall…
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Related to #1
We have developed crosslinkers with asymmetric cleavage sites that produce twin doublet peaks which we rely on to isolate CSMs that contain crosslinks. Are there any plans to incorpo…
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Hello Dear developer,
I tried to use your trained model to predict RNA cleavage sites. I got errors because of FutureWarning and numpy dtype issue. The run failed due to incompatible shape of t…