User: amonida

gravatar for amonida
amonida10
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Location:
United Kingdom
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11 months, 2 weeks ago
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2 years, 11 months ago
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Posts by amonida

<prev • 15 results • page 1 of 2 • next >
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News: Ensembl 87 is out!
... Hi all The new Ensembl marts for release 87 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensembl_mart_87 <- useEnsembl(biomart=“ensembl") Change affecting all marts: Species dropdown now displays species common name instea ...
biomart news ensembl ensemble mart ensembl mart written 11 months ago by amonida10
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Answer: A: Error: 1: Extra content at the end of the document in using biomaRt
... Hello, Are you using the main Ensembl site as your BioMart host? If so please note that the Ensembl site is currently down due to data centre maintenance (http://www.ensembl.org/index.html). You can use one of our mirror sites asia.ensembl.org, uswest.ensembl.org, useast.ensembl.org) for your biom ...
written 14 months ago by amonida10
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Comment: C: biomaRt - getBM - biomart= ENSEMBL_MART_FUNCGEN !!! NOT WORKING!!!
... Hi Juan, Sorry you're having problems with Ensembl BioMart. Unfortunately the performance does get affected when requesting features on high of regions, this is something that we are aware of and are actively trying to fix as Dan pointed out. Our benchmarking so far has shown that a limit of 500 is ...
written 17 months ago by amonida10
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Comment: C: Ensembl release 84 is out!
... Hi Ariel, Glad you've identified the source of the issue. Please let us know if you come across any Ensembl related issues in the future. Best regards, Amonida -- Amonida Zadissa Ensembl Production Team EMBL-EBI Hinxton England On 20/04/2016 20:39, arielpaulson [bioc] wrote: > Activity on a ...
written 19 months ago by amonida10
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Comment: C: Ensembl release 84 is out!
... Hi Ariel, Sorry for the late reply. Can you please paste in the exact command line you're running as I can't reproduce the error message you're getting. Below is what I get when testing the examples from Ensembl website (http://www.ensembl.org/info/data/biomart/biomart_r_package.html): > libr ...
written 19 months ago by amonida10
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Comment: C: Ensembl release 84 is out!
... Hi Arial The problem is with the formatting of the command. The first double-quote in the command is causing the issue. If you replace it with plain double-quotes the command should work fine: ensembl_mart_84 <- useEnsembl(biomart="ensembl") You can also use single-quotes: ensembl_mart_84 < ...
written 19 months ago by amonida10
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News: Ensembl 83 is out!
... We are pleased to announce that the latest Ensembl update (e!83) has been released: http://www.ensembl.org/ If you are using biomaRt, you can change your host to access our most recent data (With R 2.2 and Bioconductor version 3.1): ensembl_mart_83 <- useEnsembl(biomart=“ensembl") Ensembl G ...
biomart news ensembl ensemble mart ensembl release written 23 months ago by amonida10
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News: Ensembl GRCh37 release 82 - second data update
... Dear all, We are pleased to announce that the second Ensembl data update for human GRCh37 (e82) has been released on http://grch37.ensembl.org/index.html. Ensembl Genes 82 Renamed filters and attributes from variation to variant Renamed the "Transcript length" attribute to "Transcript leng ...
biomart news ensembl grch37 written 2.1 years ago by amonida10
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Answer: A: biomaRt fails for M.musculus annotation, Ensembl version 80
... Hi Sarah, Sorry that you're having problems with Ensembl data. As it happens, it seems that a redirection was not fully in place. The problem should now have been fixed already. Again, sorry for the inconvenience. Best regards, Amonida -- Amonida Zadissa Ensembl Production Team EMBL-EBI Hinxton ...
written 2.2 years ago by amonida10
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Comment: C: Getting a list of all tRNA encoding genes for an organism?
... Hi Johannes, Your assumption is correct; we don't annotate tRNAs at genes in Ensembl They are stored in the simple_feature table in the Core MySQL database. As Hans pointed out earlier, they can be accessed via our API. Hope this helps. Cheers, Amonida -- Amonida Zadissa Ensembl Production On 01 ...
written 2.6 years ago by amonida10

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