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Create a check that compares the numbers of genes with a specific data type in the data source file with the number of genes with that type of data in the gene descriptions file.
Example-the number o…
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Equivalence and orthology relationships may point to 'orphan' uris - i.e., uris that are created by the equivalence/orthology relationship and do not exist in the graph. Need to incorporate tests and/…
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Hi, I want to use OrthoFinder to study orthology relationships for all genes in multiple species.
I don't clearly understand the one-to-one relationships. I think the number in OrthologuesStats_one-…
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Hi,
As I'm trying to run FMP_download.pl, I added usearch path. (Because I use a Mac, I can't use diamond).
I was wondering is it better to build usearch db for blast at this step or I can simply …
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Chris and I met this week and went over the subset of KEGG BRITE that would be useful for NMDC functional search.
The suggestion yesterday was to include 1.2, 1.3, 1.4, 1.5, 1.6
my new suggestion i…
aclum updated
2 months ago
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Hi David,
I have been trying to run orthofinder with about 70 plant proteomes on a HPC cluster, and keep running into memory issues
Here's an example of my command as part of a SLURM script and …
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We have no yeast gene orthology info, e.g
https://api.monarchinitiative.org/api/bioentity/gene/SGD%3AS000003865/homologs/?rows=20&fetch_objects=true
It is in the panther species list:
https://g…
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- **Process this after processing EBI files** (#840)
The previous Alliance of Genome Resources Disease dataset were for `mouse` and `rat` only and dataset without info header. The previous file was…
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bench marking standard
https://github.com/qfo/benchmark-webservice
https://orthology.benchmarkservice.org/proxy/
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Follow up on #365
I think we need to recreate the symbolic link and make it point to the older folder (2021-01)
FYI - @kmartinez834