User: Mike Smith

gravatar for Mike Smith
Mike Smith1.0k
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1,010
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
11 hours ago
Joined:
6 years, 10 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 56 results • page 1 of 6 • next >
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Answer: A: BiomaRt: archive version of ensembl not working
... Emily's answer is correct, but you can also use the following which may be easier to remember than specifying the archive URL directly: mart <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = "92") ...
written 7 days ago by Mike Smith1.0k
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... If you're trying to run exactly the same query, but providing a list of GO ids then it expected you will get an error (or at least no results). The `filters` argument defines the column in the database you want to search. If you're asking to search a column containing gene IDs or symbols, but look ...
written 29 days ago by Mike Smith1.0k
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Answer: A: How to extract all attribute from Biomart?
... It's really not a sensible idea to try and use **biomaRt** to do this. Literally nothing about the system (the **biomaRt** package and the BioMart framework) was designed to provide data on that scale. If you want all the data in Ensembl for a particular species try getting it from the FTP site (h ...
written 5 weeks ago by Mike Smith1.0k
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Comment: C: BioMart: connection fails
... If you're using the same package version then there shouldn't be any difference between which operating system you're using. However the code has change quite a bit across the last ver versions, so I would make sure you are using the latest version (2.38.0) and R 3.5. ...
written 9 weeks ago by Mike Smith1.0k
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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 3 months ago by Mike Smith1.0k
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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 4 months ago by Mike Smith1.0k
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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 6 months ago by Mike Smith1.0k
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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 6 months ago by Mike Smith1.0k
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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 6 months ago by Mike Smith1.0k
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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 6 months ago by Mike Smith1.0k

Latest awards to Mike Smith

Guru 9 days ago, received more than 100 upvotes.
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 3 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 6 months ago, created an answer with at least 3 up-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
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 7 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 8 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 10 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 10 months ago, created a post with more than 5 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
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term

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