User: Mike Smith

gravatar for Mike Smith
Mike Smith1.1k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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4 hours ago
Joined:
7 years ago
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Posts by Mike Smith

<prev • 61 results • page 1 of 7 • next >
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Answer: A: Error in biomart connection
... That particular Ensembl archive is no longer available. You can view the list of available archives by following the link in the error message (you'll be redirected to an appropriate page) or by using the `listEnsemblArchives()` function in **biomaRt** e.g. > biomaRt::listEnsemblArchives() ...
written 7 days ago by Mike Smith1.1k
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Answer: A: why does my biomaRt query return inconsistent dataset lists?
... 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 are seeing. See https://support.bioconductor.org/p/104025/#104043 or https://www.biostars.org/p/289654/#289861 for more details. ...
written 17 days ago by Mike Smith1.1k
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Comment: C: Different results from biomaRt query and search in GTF
... You can also use the ensembldb package (https://bioconductor.org/packages/release/bioc/html/ensembldb.html) which will let you use a offline version of the Ensembl data (so no network issues) but in a database format you can construct all sorts of queries for. ...
written 17 days ago by Mike Smith1.1k
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Answer: A: How can I download data from plants.ensembl.org using wget in biomart?
... This is a pretty unusual way to query Ensembl, typically people use the Perl API or biomaRt R-package, which should make constructing queries a lot easier, but if this suits your workflow then great. I don't know how this is different from what you're trying, but this works for me: wget -O res ...
written 5 weeks ago by Mike Smith1.1k
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Answer: A: Different filters for wheat in biomaRt package and website
... Emily's answer is exactly how I go about diagnosing problems with the **biomaRt** package. Checking the XML via the web interface is always my first port of call for something like this. I thought I'd advertise the recently added the `searchDatasets()`, `searchFilters()` and `searchAttributes()` f ...
written 7 weeks ago by Mike Smith1.1k
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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 9 weeks ago by Mike Smith1.1k
2
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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 3 months ago by Mike Smith1.1k
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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 3 months ago by Mike Smith1.1k
0
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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 4 months ago by Mike Smith1.1k
2
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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 6 months ago by Mike Smith1.1k

Latest awards to Mike Smith

Scholar 7 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 17 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 4 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Guru 10 weeks ago, received more than 100 upvotes.
Appreciated 3 months ago, created a post with more than 5 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
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 5 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 8 months ago, created an answer with at least 3 up-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
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 9 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
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
Appreciated 12 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio

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