User: Steffen Durinck

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Posts by Steffen Durinck

<prev • 58 results • page 1 of 6 • next >
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Biomart with human genes NCBI 35
... Hi Marco, There is a better attribute to query the start and end positions of genes, use the following query: gene.list <- getBM(c("entrezgene","chr_name","chrom_start","chrom_end"), filters="chr_name",values=1, mart=ensmart) Best regards, Steffen -----Original Message----- From: marco zu ...
microarray cancer biomart written 10.4 years ago by Steffen Durinck580
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Answer: A: Biomart with human genes NCBI 35
... Hi Marco, James, Thank you for reporting this. It looks indeed like something goes wrong when using getFeature with biomaRt in MySQL mode, I'll investigate what causes this and provide a fix as soon as possible. Part of the error is due to different naming of the attributes in different versions o ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: intron sequences from biomaRt
... Hi Dario, If the BioMart web server would implement this, it would become readily available in R, but the are currently no plans for them to do this and neither do we currently intend to implement this ourselves in biomaRt (unless you want to contribute this function;) ). Would my previous suggest ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: changes in biomart database ?
... Dear Marco, Thank you for reporting this. This is a bug, the large number 2500000000 gets replaced in R by 2.5e+09 which is not understood by the webservice at the Ensembl end. Try putting the number between quotes so it doesn't get converted in R and your query should work. gene.list <- getFea ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: Biomart with human genes NCBI 35
... Dear Marco, Selecting archived versions is currently only possible using biomaRt in MySQL mode and will become available soon in web service mode. To see the available archives do: listMarts(mysql=TRUE, archive=TRUE) To connect to a previous version (e.g. Ensembl 44) you have to do: ensembl = u ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: intron sequences from biomaRt
... Dear Dario, No there is currently no possibility to select intronic sequences directly. You could request this at helpdesk at ensembl.org and see if they want to add this feature in future versions of Ensembl. For now the only way to do it with biomaRt would be to retrieve the transcript or gene ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: getting Locus Link ids from gene symbol
... Hi Alex, You could use the biomaRt package for this, here the code to do it: >library(biomaRt) >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") >map = getBM(c("hgnc_symbol","entrezgene"), filters=c("hgnc_symbol","with_entrezgene"), values=list(c("Btk","Casp8"),TRUE), mart=en ...
written 10.4 years ago by Steffen Durinck580
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Answer: A: Problem using useMart with local DB
... Hi Alessandro, From biomaRt 1.10.0 you have to specify the port as well. Default for MySQL is 3306 so try: ensembl=useMart("ensembl_mart_44", dataset="hsapiens_gene_ensembl",host="localhost", user="*****", password="******", local = TRUE,mysql = TRUE, port="3306") That should work. Cheers, Ste ...
written 10.5 years ago by Steffen Durinck580
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Answer: A: biomaRt - retrieve chrom location
... Dear Joao, Try: a <- getGene(id = unique_UniGeneCluster[,1], type = "unigene", mart = ensembl) Also if you are only interested in the chromosomal positions you might want to use the more general getBM function. Your query would look like this: a = getBM(c("unigene","ensembl_transcript_id","c ...
written 10.5 years ago by Steffen Durinck580
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Answer: A: convert IMAGE Clone ID to Entrez Gene ID
... Dear Joao, IMAGE clone IDs are not present in the Ensembl BioMart database. You could do the mapping here: http://genome-www5.stanford.edu/cgi-bin/source/sourceBatchSearch Best regards, Steffen Jo?o Fadista wrote: > Dear all, > > I would like to know if there is any package (perhaps b ...
written 10.5 years ago by Steffen Durinck580

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