User: arielpaulson

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arielpaulson20
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1 year, 6 months ago
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1 year, 7 months ago
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Posts by arielpaulson

<prev • 5 results • page 1 of 1 • next >
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Ensembl bacteria not accessible from biomaRt
... Hi, I need to know how to access Ensembl bacteria via biomaRt, if it can be done.   I can access all the non-vertebrate marts (fungi, plants, metazoa, protists) by their respective ensembl.org subdomains, but not bacteria.  When I try: > listMarts(host="bacteria.ensembl.org") I get this craz ...
biomart ensembl written 18 months ago by arielpaulson20 • updated 18 months ago by Martin Morgan ♦♦ 20k
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Ensembl version from non-vertebrate biomaRt
... Hi, I used to be able to get Ensembl version numbers from non-vertebrate marts, but sometime between Ensembl 81 and 84 this has been lost.  For instance, vertebrate marts clearly show their version numbers: > listMarts(host="www.ensembl.org")                                     biomart         ...
biomart ensembl written 18 months ago by arielpaulson20 • updated 18 months ago by Dan Staines70
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Answer: A: Ensembl release 84 is out!
... Hi Amonida, I've discovered the problem is on our end.  We have a CentOS 6 sitewide environment, but someone has built the sitewide biomaRt package on an "experimental" server running CentOS7 -- apparently -- because biomaRt will only work on that server.  Everywhere else it fails like:  > libr ...
written 19 months ago by arielpaulson20
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Answer: A: Ensembl release 84 is out!
... Hi Amonida, The error message in my post shows that this is not a quoting problem. I cut and pasted the blog-post code into reply, but in the code I ran, I had replaced the quotes.  Bad quotes would return a completely different error message, since R would not be able to parse the function argumen ...
written 19 months ago by arielpaulson20
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Answer: A: Ensembl release 84 is out!
... Trying the above command -- useEnsembl(biomart=“ensembl") -- today on R 3.2.2 and R 3.2.0, it does not work, gives error "Incorrect BioMart name, use the listMarts function to see which BioMart databases are available".  Also, using listMarts() with core host "www.ensembl.org" returns a data frame w ...
written 19 months ago by arielpaulson20

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