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Hello,
I am trying to use the i-ADHoRe tool for human and mouse using the output files from OrthoFinder. For this purpose, I created the `blast_table=Orthologs.list` file, which looks like:
ENSG0000…
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From Damian:
> (1) Disease IDs, terms and HPO annotations
> (2) Mouse Strain ID, Gene ID, Gene symbol and MP annotations (I also need the IMPC annotations to be in there and only single gene reco…
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For example, I want to use the agaricales_odb10 as reference database to pick single copy orthologs, how can I change the Fungi_odb10 to Agaricales_odb10?
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@adkinsrs @JPReceveur
I talk to 2 persons in the lab and we agreed that the sentence below should be changed to one of the following:
- Neither the given gene symbol(s) nor corresponding orthologs …
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Hi,
(thanks for a great application)
Toxic model averaging works fine, as far as I can judge, but I never get any GO/reactome/bioplanet results for Danio rerio although mouse and fruitfly works fine…
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- [x] Cookies
- [ ] Manager
- [ ] DatabaseManagement
- [x] ProjectManagement
- [ ] Orthologs
- [ ] Align
- [x] Blast
- [ ] Genbank
- [x] CompGenetics
- [ ] Phylogenetics
- …
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This is an old issue (#114) which does require a neat solution.
Orthologs are grouped in search results by their UniProt name (ID) prefix, which usually works but fails sometimes, as it is not fool pr…
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Hi,
I was wondering if the SHOOT website has an API or some way to submit proteins via command line? I have a few hundreds genes I'd like to run through SHOOT to identify orthologs.
Thanks
Jon
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The UI may be fiddly, but we should at least allow people to do things like this via the command line. It shouldn't be hard using e.g. scigraph-python
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Hi, I am facing the below mention issue. I have tried to go through the module assess_specific_genes.nf and unable to resolve this on my own and would request your help. I am trying this with the test…