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Hi,
This is a follow-up step after https://github.com/PMBio/deeprvat/issues/117#issuecomment-2278887881.
(I'm opening a new issue so that each issue can be more single threaded. If you prefer me…
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Hi,
I have a question about the usage of compareCluster function. Is it only meant to be used to compare gene sets between different experimental conditions in the same species. Or can it also be u…
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Hi there,
I was browsing around the zoonomia data portal and found this [link](https://cgl.gi.ucsc.edu/data/cactus/241-mammalian-2020v2-hub/documentation/zoonomiaGenes.html) saying that gene predic…
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The following GFFs either lack Note: attributes or have none containing GO: terms. (@maxglycine it is indeed a common problem with a number of Glycine and Medicago annotations.) Please fix.
- [ ] A…
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**Describe the bug**
I am trying to run `download_genome_annotations` in the snakemake pipeline but unable to produce genome annotation and chromsizes tsv files.
**To Reproduce**
`scenicplus prep…
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* **InterPro ID / label**
IPR012080
* **Example sequences with problematic annotation (ID + gene/protein name):**
https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P78780&aspect=biolo…
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Hi!
Lately, I experienced fragmented gene annotations in terms of two (or more) ORFs that are in close proximity and are annotated with homology to the same gene. In such cases, Prokka ads an `_n` …
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Hello!
I have been using TOGA lately for transferring hg38 gene annotations to a newly constructed genome and it looks good so far! However, I do notice that annotations for non-coding RNAs such as…
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Aim: Import high confidence GO annotations (GO term to gene) for GO terms directly linked to CL terms - bidirectional by and object property restriction.
The links from GO terms to Genes (proteins)…
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Hi Joelle!
I am also running a gene-based test and this error keeps on appearing. I took the reference of the previous similar question and in my case the two files have exact the same format. Bu…