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### Description of feature
Instead of attached on specific statistical test to a workflow, let them run on any the generalized stand_pep/stand_prot files, then providing an updated version of these f…
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We need to add PROVEAN in order to assign PP3 (http://provean.jcvi.org/index.php). Someone please look into this and determine how to add wrap this into oncotator
We need to run all the variants vi…
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Hi,
Thanks for this amazing tool. I think it's pretty useful in searching hypothesized non-ribosomal peptides.
I have some confusion in the result interpretation. In the output, it has a column…
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This issue was left unanswered in the standard. Let's come up with a proposal, implement it, and see if the committee for the standard has any issues with it.
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Hi Vadim,
I have been using Dia-NN through FragPipe to analyze custom PTMs (one is in UniMod but the other is not). I managed to run it but PTMProphet has to be disabled because it has an issue wit…
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This is more of a theoretical question than a practical one: I have never worked with C-terminal PTMs before. But I find the explanations of the syntax for specifying where they apply in MSFragger sli…
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#### Current behavior:
22 genes are discovered to be uncorrelated with their corresponding reactions in `Leukotriene metabolism`.
| Gene | UniProtID | Reaction| GPR| Correlation| Manually …
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@jchodera and I found in issue with the geometry proposals in WT RBD:ACE2 N501Y and beta variant RBD:ACE2 Y501N -- the CA chirality is R, not S. This happens in both apo and complex.
Note that for th…
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I am applying SILAC modifications to a spectral library using these options:
--fixed-mod SILAC,0.0,KR,label
--lib-fixed-mod SILAC
--channels SILAC,L,KR,0:0; SILAC,H,KR,8.014199:10.008269
--or…
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I am now doing some intact protein analysis and it was recently demonstrated that when you fragment proteins you produce a lot of internal fragments:
http://www.ncbi.nlm.nih.gov/pubmed/25716753
cons…