User: Thomas Maurel

gravatar for Thomas Maurel
Thomas Maurel570
Reputation:
570
Status:
Trusted
Location:
United Kingdom
Last seen:
5 days, 19 hours ago
Joined:
4 years, 9 months ago
Email:
m*****@ebi.ac.uk

Bioinformatician - Ensembl Production Team

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom

Posts by Thomas Maurel

<prev • 92 results • page 1 of 10 • next >
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Answer: A: Error in getBM of biomaRt package
... Hello, I am afraid that we had a DOS attack affecting our www.ensembl.org marts on Friday. The services were restored shortly after the attack. Apologies for any inconveniences caused.  Kind Regards, Thomas ...
written 16 days ago by Thomas Maurel570
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Answer: A: Getting errors with makeTxDbFromBiomart
... Hello, I am afraid that only the 69 vertebrate species and the 16 mouse strains MySQL files can be found at this location: ftp://ftp.ensembl.org/pub/current_mysql/. The other ensembl divisions can be found on their respective FTP site spaces: Plants: ftp://ftp.ensemblgenomes.org/pub/release-34/ ...
written 28 days ago by Thomas Maurel570
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Comment: C: adding attributes affects number of results returned
... Dear Mike, You are right, rs368991480 don't have any associated phenotypes so we can't bring in ENSG00000175445 associated gene name. Regarding the issue with rs368991480 being dropped from the result, I changed the way we generate our phenotype table so for our next release (e!88), you will get so ...
written 5 weeks ago by Thomas Maurel570
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Answer: A: adding attributes affects number of results returned
... Hi Mike, Oh I see sorry, I got confused with an other associated gene name attribute. I guess what I gave above is a temporary solution then ;-). Yes, this look like a bug from our side, rs368991480 seems to be missing from our BioMart phenotype table. I will investigate and see if we can get it f ...
written 6 weeks ago by Thomas Maurel570
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Comment: C: adding attributes affects number of results returned
... Dear Mike, I had a look on the Ensembl biomart Interface and I get a different behaviour than what you have reported below with the biomaRt package. If I filter on the following variants rs368991480,rs1082714,rs1085093 and ask for the refsnp_id and ensembl_gene_stable_id attributes, I get the thre ...
written 6 weeks ago by Thomas Maurel570
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Answer: A: biomaRt - rice genes database not working
... Dear Maia, You will need to connect to the Ensembl plants marts to be able to query Rice: > listMarts(host="plants.ensembl.org") biomart version 1 plants_mart Plant Mart 2 plants_variations Plant Variation Mart > gramene = useMart("plants_mart", dat ...
written 4 months ago by Thomas Maurel570
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Answer: A: Biomart getLDS error
... Just to let you know that the US West, US East and Asian mirrors have now been fixed too. Thank you for your patience. Best Regards, Thomas ...
written 4 months ago by Thomas Maurel570
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Answer: A: Error in biomaRt User Guide example Task 11
... Dear all, Just to let you know that the US West, US East and Asian mirrors have now been fixed too. Thank you for your patience. Best Regards, Thomas ...
written 4 months ago by Thomas Maurel570
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Answer: A: biomaRt error while querying homo sapien structural variants
... Dear all, Just to let you know that the US West, US East and Asian mirrors have now been fixed too. Thank you for your patience. Best Regards, Thomas   ...
written 4 months ago by Thomas Maurel570
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Answer: A: Biomart getLDS error
... Just to let you know that we have now pushed a fix to our main website www.ensembl.org, you can access it by running: human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org") or human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")  We will f ...
written 4 months ago by Thomas Maurel570

Latest awards to Thomas Maurel

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biomaRt: no access to Ensembl_75 (GRCh37.p13)
Scholar 10 months ago, created an answer that has been accepted. For A: how to use biomaRt with ensembl build 37
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: how to use biomaRt with ensembl build 37
Appreciated 20 months ago, created a post with more than 5 votes. For Ensembl release 80 is out!
Appreciated 21 months ago, created a post with more than 5 votes. For Ensembl release 80 is out!
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: how to use biomaRt with ensembl build 37
Scholar 2.3 years ago, created an answer that has been accepted. For A: how to use biomaRt with ensembl build 37
Autobiographer 2.4 years ago, has more than 80 characters in the information field of the user's profile.

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