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Hi,
When running test_diff the order of factors/covariates in the design matrix affects the final analysis.
I have put this issue up on BioStars: https://www.biostars.org/p/9588610/#9602501 and …
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Thank you for developing Chroma. Chroma is such an excellent generative AI tool for de novo protein design.
I would like to inquire about how one can use Chroma to design new functional proteins (no…
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### Describe the bug
At least some proteins need normalization - e.g. ACE2:
```
UniProtKB:Q9BYF1 ACE2 pharmgkb|intact|go-cams
NCBIGene:59272 ACE2 zhou_host_proteins|SciBite-CORD-1…
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Currently we don't differentiate between genes and proteins, we just lump them all under gene. However, most go annotation is at the protein level. When we have a go annotation, and we ask quickgo …
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Hello,
While working on the orthogroups PR, I ran into an issue with the way proteins are managed in GNB.
Currently, there are no 'proteins' in DB. When accessing a gene, proteins sequences are …
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Could you help me find some data? I've looked through all the proteoform datasets and I can't seem to find examples of proteins that have a glycosylation range rather than a single site/residue. Is th…
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In the published models (especially those using the "European (P-gp modified, CYP3A4 36 h)" individual), I found some differences in the expression profiles from the values stored in the database.
…
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To do when reviewing proteomics collections. Currently there is not an enforced pattern for [best_protein](https://microbiomedata.github.io/berkeley-schema-fy24/best_protein/) or [all_proteins](https:…
aclum updated
26 minutes ago
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## The issue
Currently, we don't do a good job supporting multiple types of `pranges`. We have on one side an example were `pranges` store peptides along proteins. With the new `EnsDb` access to p…
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Hello!
I'm having a slight issue with the annotations generated by EGAPx. When I translate the CDS into a protein sequence, I'm seeing a lot of premature stop codons. This is a species where I am s…