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Thank you for developing such a promising software for the scientific community.
I tried running Alphalink2 with several datasets, including the rpoa-rpoc dataset used in the bioRxiv manuscript but …
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for summarizing query path results during evaluation. For example, annotating pathway figures with terms from the Pathway Ontology will allow BTE users to filter genes by hierarchically-organized path…
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**- Describe the feature:**
I haven't found a direct way to do this, but am trying to set certain amino acids to only be searchable with variable mods. For instance looking at methylation on say 3 ly…
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## BLAST search
Let's introduce **BLAST** search feature support.
**Displaying BLAST search results for *read*/*feature* sequence**:
- User clicks on *read* (or any other feature) and selects *…
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In trying to train ProteinBert, I've received the following error:
```
indices[31,1] = -127 is not in [0, 290)
[[{{node model/embedding-seq-input/embedding_lookup}}]] [Op:__inference_train_functi…
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The VRS 2.0 specification uses a property (`ga4ghDigest.keys`) to indicate keys that are used in creating VRS computed identifiers. This has the same functionality as the SeqCol `inherent` attribute.
…
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Hello,
I am working with the AminoAcid class (deeprankcore/models/amino_acid.py) because the Residue class (deeprankcore/models/structure.py) requires it, and running into an issue. The common 20 a…
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Coronaspades' gene_clusters file are here: `s3://serratus-public/assemblies/dicistro/gene_clusters/`
Other coronaspades files: `s3://serratus-public/assemblies/dicistro/other/`
4921 assemblies mad…
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Hi guys, thanks for this great work :)
I see that your fine tuning examples (in the appended notebook) don't have GO annotations to go together
with the amino acids sequences. Can you explain how th…
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This function does not attempt to determine which pairs of points from either cloud correspond. Instead, it infers them from the order of the arrays.
I wonder if there exisits methods that determine …