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A neoantigen prediction pipeline from [Hammerlab](https://github.com/hammerlab/epidisco), mostly making use of the [Isovar](https://github.com/openvax/isovar) tool from OpenVax.
This seems to be on…
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As noted by @andrewsu, GTOPDB:836 is showing up as a SmallMolecule, (it's coming that way out of automat, but that's because NN is tagging that entity as a SmallMolecule).
It looks like we're calli…
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This issue is related to #136, which happens due to a but in the C++ `RcppIndent::getScores()` function, that counts the number of cvParams on the first `SpectrumIdentificationItem`, but then crashes …
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Dear RFdiffusion Team,
First, I want to express my appreciation for your work!
I am reaching out with a specific question regarding the customization of the binder design process. Specifically, …
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Hi MetaMorpheus developers,
Is there any tutorial for running the MM tool for o-linked GlycoProteomics? I tried the MM for few o-linked enriched raw files (HCD fragmentation) using two tasks: 1- Cal…
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We are planning to deprecate certain features of El-MAVEN that are either no longer useful to the community or fall outside the scope of El-MAVEN. [See discussion](https://github.com/ElucidataInc/ElMa…
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Hi,
after a long time, i think i can train my PointNet on the refined-dataset. But as you said, the indicator is after a manner.So i turn my eyes to bigger dataset.
In the paper , you descr…
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Currently, fragmentation masses are determined as a vector of masses, e.g. ``. The index of the position in the vector is used to determine the length of the peptide. However, if there are NLs interm…
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Hi all,
Sean pointed out to me that the current mzid specifications appear to rule out
the coding of de novo approaches. When we made the transition from mzid 1.0 to
1.1, we made PeptideEvidenc…
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Dear @nkurzaw,
when I use the package function `import2Dataset()` in combination with replicated measurements (each temperature * drug combination was measured twice) it crashes. The function call …