User: Christophe Dessimoz

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

<prev • 39 results • page 1 of 4 • next >
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Answer: A: OMA error - download from gene ontology not working 404
... 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 Dessimoz530
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Answer: A: Getting the highest taxonomy in the HOG database for a given OMA gene id
... 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 Dessimoz530
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Comment: C: Use OrthoDB to retrieve the orthologs between human and bacteria
... https://omabrowser.org/oma/release/ ...
written 4 weeks ago by Christophe Dessimoz530
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Answer: A: Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree
... 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 Dessimoz530
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Answer: A: Use OrthoDB to retrieve the orthologs between human and bacteria
... 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 Dessimoz530
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Job: Postdoctoral position in evolutionary bioinformatics in Switzerland
... 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 ...
postdoc phylogenetics job phylogenomics written 5 months ago by Christophe Dessimoz530
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Comment: C: Trying to hack OMA to do specific All-v-All searches
... Ahhh adrian.altenhoff beat me to it! ...
written 6 months ago by Christophe Dessimoz530
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Answer: A: OMA - How to retrieve orthologs of only one representative of each taxonomy rank
... 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 Dessimoz530
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Answer: A: Trying to hack OMA to do specific All-v-All searches
... 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 Dessimoz530
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Answer: A: How export HOG viewer tree with orthologs in OMA
... 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 Dessimoz530

Latest awards to Christophe Dessimoz

Scholar 6 months ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 22 months ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Scholar 22 months ago, created an answer that has been accepted. For A: Can OMA calculate orthologs for single query sequence?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Appreciated 2.2 years ago, created a post with more than 5 votes. For The Gene Ontology Handbook (open access)
Scholar 3.0 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Popular Question 3.2 years ago, created a question with more than 1,000 views. For (Senior) Research Associate In Bioinformatics And Comparative Genomics At Ucl, London
Scholar 3.2 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone
Scholar 3.3 years ago, created an answer that has been accepted. For A: Details of OMA Running Process - OMA standalone
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Details of OMA Running Process - OMA standalone

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