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For my project I am wanting to look at how specific genes are regulated, so will likely need gff and fasta files that include full UTRs rather than just a buffer.
Pombase has separate fasta files fo…
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Gene.mirna was used for 37, not used in 38. Do we still need these data? `mirna.txt` is not on the download list, so it's not being loaded anymore.
- [ ] remove mirna from [GeneParser.java](https:/…
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Going forward, I will add problems to this Googlesheet:
https://docs.google.com/spreadsheets/d/1AME11i0L9TtGqMINUECFKgchKfZWNdk7RvaGM6VyeBY/edit#gid=0
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Right now the[ URL for MotifFeatures.gff.gz is incorrect](https://github.com/opencb/cellbase/issues/466). However the file is still created with a size of zero:
```
-rw-r--r-- 1 julie julie …
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Please provide as much information as you can:
* **Suggested term label:**
Negative regulation of GDP-mannose biosynthetic process
* **Definition (free text)**
Any process that stops, prevent…
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Hi,
Thank you for this wonderful tool. I have a few questions regarding the input and output.
1. I understand that --match finds a drug that matches the DEG files used, but what does the option with…
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from
https://github.com/pombase/canto/issues/2482#issuecomment-878120963
Note to self:
We also need to consider if this will work for
protein A directly inhibits [protein B protein-binding prot…
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Hi!! Thanks for this easy to install and easy to use CLI tool for functional identification. I have few queries:
1. Can I use proteinfer for organism ranging from Bacteria to Eukaryotes? If so do w…
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Frequently certain generic terms like "expression" and "overexpression" are getting flagged as entity modifications in the REACH output. This is tricky for us because this ends up getting treated as a…
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Hello,
We have a bunch of GO_REFs that were created for TermGenie term creation, that essentially describe the branch under which the term is (see table below).
All terms with those GOREFs als…