User: Mike Smith

gravatar for Mike Smith
Mike Smith820
Reputation:
820
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
1 week ago
Joined:
6 years, 4 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 50 results • page 1 of 5 • next >
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Answer: A: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... There was an issue with **biomaRt** that manifested when Ensembl release 91 introduced datasets with apostrophes in e.g. "Ma's Night Monkey" which would lead to the error you were seeing. See https://support.bioconductor.org/p/104025/#104043 or https://www.biostars.org/p/289654/#289861 If you were ...
written 9 days ago by Mike Smith820
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Comment: C: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... Can you update your post to include the output of the command `sessionInfo()` so we can see what version of R & biomaRt you are using? ...
written 9 days ago by Mike Smith820
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Answer: A: Find all rsid synonyms for a list of rsids
... You can do this using R and **biomaRt**. Here's an example. First lets create two example sets of SNPS. Between these the first pair are identical, the second pair are synonyms to each other, and the third pair are distinct. snps1 <- c('rs4844600', 'rs4266886', 'rs6656401') snps2 &l ...
written 24 days ago by Mike Smith820
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Comment: C: Obtaining rsIDs using BiomaRt or linux
... You can improve the speed of this approach by noting that you can use a vector of values if you use the `chromosomal_region` filter. This requires that you supply the SNP coordinates in the form *chrom:start:end*. You then don't need a loop or the `do.call` expression, just a single call to `getBM ...
written 24 days ago by Mike Smith820
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Answer: A: How to avoid annotating multiple genes to a single CpG locus?
... I think this is non-trivial. If you look at your PCDHGC example (http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000240184;r=5:141475207-141513719) Ensembl has multiple genes spanning the same region. I don't know the reasoning behind why these are separate genes rather than tran ...
written 5 weeks ago by Mike Smith820
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Answer: A: BioMart: connection fails
... As Emily has said, parts of Ensembl are down right now. This includes the archive sites and the BioMart interface at the main site. You can check this just by visiting in a browser (http://www.ensembl.org/biomart/martview?redirect=no) - at the moment you get an error page. However you can use one ...
written 9 weeks ago by Mike Smith820
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Answer: A: Query Genes within regions
... You're correct that a weakness of **biomaRt** is that you can't match the results with a specific part of the query, it just dumps back everything that matched at least once, and querying with each region separately isn't very quick if you have thousands of regions. If you want to do this in R, the ...
written 11 weeks ago by Mike Smith820
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Comment: C: Where can I download homo sapiens gene locations file including ensembl gene id,
... You can use a programmatic interface to BioMart like [biomaRt][1] and then your script records the steps you took to get the data out. [1]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 12 weeks ago by Mike Smith820
3
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Answer: A: Mapping Ensembl Gene IDs with dot suffix
... Here's an example of doing the conversion using **biomaRt**. You can use the versioned IDs you've got, but you'll see it's better the remove the version numbers. First, we'll load **biomaRt** and use your example IDs. library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsa ...
written 4 months ago by Mike Smith820
5
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Answer: A: Get gene symbols from gene ids for mouse using BioMart
... The filter you need is `mgi_symbol` e.g. library(biomaRt) ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl") mouse_gene_ids <- "0610009B22Rik" foo <- getBM(attributes=c('ensembl_gene_id', 'external_gene_name'), ...
written 4 months ago by Mike Smith820

Latest awards to Mike Smith

Scholar 17 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 8 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 4 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 4 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 6 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term

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