User: Mike Smith

gravatar for Mike Smith
Mike Smith850
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850
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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3 hours ago
Joined:
6 years, 6 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 52 results • page 1 of 6 • next >
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Answer: A: Trying to add ensembl_transcript_id using Biomart
... I think the reason you're getting some NA values is because the gene IDs you are using (taken from `rownames(counts)`) include a version number at the end e.g. "ENSMUSG00000000001.4". Your **biomaRt** query then doesn't match these as your filter specifies the non-versioned IDs to search. Here's a ...
written 5 days ago by Mike Smith850
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Answer: A: Biomart package listFilter function with with_mirbase vs other mir information
... The two filters that start `with_` are boolean filters, meaning that take either `TRUE` or `FALSE`. You can use these to return only the entries stored in Ensembl that have a particular type of ID. So if you want the list of all entries that have a mirbase ID you would use the `with_mirbase` filte ...
written 25 days ago by Mike Smith850
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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 10 weeks ago by Mike Smith850
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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 10 weeks ago by Mike Smith850
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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 12 weeks ago by Mike Smith850
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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 12 weeks ago by Mike Smith850
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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 3 months ago by Mike Smith850
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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 4 months ago by Mike Smith850
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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 4 months ago by Mike Smith850
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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 5 months ago by Mike Smith850

Latest awards to Mike Smith

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 11 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
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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
Appreciated 6 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 6 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 6 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 6 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
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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