User: Steffen Durinck

gravatar for Steffen Durinck
Reputation:
530
Status:
Trusted
Location:
Last seen:
3 years, 4 months ago
Joined:
6 years, 9 months ago
Email:
d**************@gene.com

Posts by Steffen Durinck

<prev • 52 results • page 1 of 6 • next >
0
votes
1
answers
892
views
1
answers
Comment: C: Biomart annotation
... Also, you can specify the biotype filter so you only retrieve protein coding genes by changing your query to: entrez_id <- getBM(attributes = c("ensembl_gene_id", "entrezgene", "hgnc_symbol"), filters = c("ensembl_gene_id","biotype"), ...
written 3.3 years ago by Steffen Durinck530
0
votes
2
answers
2.0k
views
2
answers
Answer: A: biomaRt proxy issues
... Thanks Enrico, I'll update the biomaRt vignette with this working code. Best, Steffen On Fri, Jun 27, 2014 at 2:10 AM, Enrico Ferrero wrote: > Bill, > > Thanks very much for this. I had proxy issues with biomaRt for the longest > time and they're finally over. > Can the biomaRt ...
written 3.4 years ago by Steffen Durinck530
0
votes
1
answers
393
views
1
answers
Answer: A: bioMart request failed
... Hi Alejandra, You can switch to the ensembl website by doing: ensembl=useMart("ENSEMBL_MART_ENSEMBL",host="www.ensembl.org ",dataset="mmusculus_gene_ensembl") Best, Steffen On Mon, Feb 24, 2014 at 1:18 PM, Alejandra Medina [guest] < guest@bioconductor.org> wrote: > > Hi > > I ...
written 3.7 years ago by Steffen Durinck530
0
votes
3
answers
493
views
3
answers
Comment: C: Problem with filtering genes in biomaRt
... Hi Thomas, A "big" query like this has never been a problem before, can you shed some light at what could be causing this? Were there some changes at Ensembl? Best regards, Steffen On Fri, Feb 7, 2014 at 2:16 AM, Thomas Maurel wrote: > Dear Pieta, > > As you have noticed in your quer ...
written 3.8 years ago by Steffen Durinck530
0
votes
1
answers
2.2k
views
1
answers
Answer: A: biomaaRt error: Extra content at the end of the document
... Hi Hari, If you go to the web page of BioMart for that specific archive you'll see that is temporarily unavailable. http://may2009.archive.ensembl.org/biomart/martview I would check again in a bit and if this site comes back, you should be able to do your queries with biomaRt again. If it is out ...
written 3.8 years ago by Steffen Durinck530
0
votes
1
answers
2.5k
views
1
answers
Answer: A: biomaRt: retrieve exon sequence, start and end positions
... Hi Tim, Not sure why you get less sequences with the getSequence query, you can add gene_exon to your getBM query though and get the sequence for all 79 by: gb <- getBM(attributes=c('ensembl_exon_id', "exon_chrom_start","exon_chrom_end","gene_exon"), filters = "ensembl_gene_id", values="ENSG000 ...
written 3.9 years ago by Steffen Durinck530
0
votes
1
answers
925
views
1
answers
Answer: A: biomaRt : cannot useMart with biomart.informatics.jax.org because host="lindon"
... Hi Mike, It looks like the MGI BioMart is not properly configured and someone should make them aware of that. You can trick the biomaRt package to still get access to the BioMart though, here's how: >mart=useMart("ensembl") >mart@host="http://biomart.informatics.jax.org/biomart/martservice" ...
written 4.0 years ago by Steffen Durinck530
0
votes
1
answers
1.3k
views
1
answers
Answer: A: getBM returns shorter vectors than values
... Hi Francesco, That is correct, biomaRt doesn't return anything if it can find it. It is designed to work just like the BioMart web services at www.biomart.orgwhich behave the same. I usually add the filter as an attribute so I can match things up and figure out what did return a result. Your query ...
written 4.2 years ago by Steffen Durinck530
0
votes
1
answers
274
views
1
answers
Answer: A: BiomaRt and archival versions of ensembl_mart
... Hi Greg, A better way to access an ensembl archive is to specify the archive URL in the host parameter like this: ensembl=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl" ,host=" jan2013.archive.ensembl.org") This will connect you to Ensembl 70 for example. To figure out which host ...
written 4.2 years ago by Steffen Durinck530
0
votes
1
answers
641
views
1
answers
Answer: A: BiomaRt useMart() issues
... Hi Burak, This was probably a temporary connection issue as I can not replicate the error. Can you try this again and see if it is resolved? Best regards, Steffen On Sat, Aug 24, 2013 at 3:43 PM, burak kutlu wrote: > Hello > There seems to be an issue with the useMart() which spits out t ...
written 4.2 years ago by Steffen Durinck530

Latest awards to Steffen Durinck

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 130 users visited in the last hour