User: Christophe Dessimoz
Christophe Dessimoz • 530
- Reputation:
- 530
- Status:
- Trusted
- Location:
- University College London
- Website:
- http://lab.dessimoz.org/
- Twitter:
- cdessimoz
- Scholar ID:
- Google Scholar Page
- Last seen:
- 16 hours ago
- Joined:
- 5 years, 3 months ago
- Email:
- c*********@ucl.ac.uk
Posts by Christophe Dessimoz
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... Thanks for reporting this problem. It indeed appears that the Gene Ontology consortium website was recently updated and the URL has changed. We will fix this and do a new release soon. Meanwhile, if you (or anyone else) is affected, here is a fix:
Locate the "darwinlib" directory. If you are runnin ...
written 16 hours ago by
Christophe Dessimoz • 530
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... There are several options. One way is to use the REST API. If you use e.g. P53_RAT as an input sequence:
https://omabrowser.org/api/hog/P53_RAT/?level=root
You can see that the level is Chordata (in the current Dec 2018 release).
If you use Python, you can use the omadb package
$ pip ins ...
written 16 hours ago by
Christophe Dessimoz • 530
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... https://omabrowser.org/oma/release/ ...
written 4 weeks ago by
Christophe Dessimoz • 530
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... The documentation of pyHam can be accessed here: https://github.com/DessimozLab/pyham
There is a tutorial here: http://lab.dessimoz.org/blog/2017/06/29/pyham
Finally, there is now an Application Note introducing the package here: https://doi.org/10.1093/bioinformatics/bty994 ...
written 10 weeks ago by
Christophe Dessimoz • 530
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... You can use OMA (http://omabrowser.org) to retrieve orthologs between human and bacteria (or indeed across domains of life in general. ...
written 4 months ago by
Christophe Dessimoz • 530
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... Postdoctoral position in evolutionary bioinformatics
===========
University of Lausanne & Swiss Institute of Bioinformatics
*Start date:* 01.11.2018 (or as soon as possible thereafter)
*Contract:* 1 year, renewable 2 x 2 years, maximum 5 years
*Activity rate:* 100%
The research grou ...
written 5 months ago by
Christophe Dessimoz • 530
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... Ahhh adrian.altenhoff beat me to it! ...
written 6 months ago by
Christophe Dessimoz • 530
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... You can use the REST API (https://omabrowser.org/api/docs), or if you are using R you could use our bioconductor package OmaDb (https://bioconductor.org/packages/release/bioc/html/OmaDB.html).
Either way, you could retrieve the taxonomy tree of all species in OMA (e.g. GET /api/taxonomy/?type=newic ...
written 6 months ago by
Christophe Dessimoz • 530
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... Hi Jason,
You found a workaround, but for the use case you describe, I think that you don't need the hack. If you run OMA standalone as a job array (see https://omabrowser.org/standalone/#schedulers), each job will get a distinct subset of chunks to process, even if there is no shared filesystem. S ...
written 6 months ago by
Christophe Dessimoz • 530
1
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... What do you mean by "exporting"? You can run the HOG viewer (which we now call "iHam") on your own OrthoXML file (e.g. exported from the OMA browser, or produced by OMA standalone) using the following code:
https://github.com/DessimozLab/iHam
Does this answer your question? ...
written 6 months ago by
Christophe Dessimoz • 530
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For Postdoctoral associate positions at the University of Lausanne, Switzerland (open call)
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For Postdoctoral associate positions at the University of Lausanne, Switzerland (open call)
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For The Gene Ontology Handbook (open access)
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