User: Mike Smith

gravatar for Mike Smith
Mike Smith330
Reputation:
330
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
15 hours ago
Joined:
5 years, 8 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 29 results • page 1 of 3 • next >
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Comment: C: 'BiocParallel' did not register default BiocParallelParams
... While I agree that there can be plenty of problems in scientific software distribution, it seems to me that here you're unfairly blaming package developers for incompatibility issues. On the two setups listed in the first post you're running the cutting edge, one month old, version of R, but trying ...
written 17 days ago by Mike Smith330
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Comment: C: Is biomaRt service down?
... To try and understand this a bit more, what to you get back if we strip away all the biomaRt interface, and just directly submit the query to the Ensembl server? You can view code to do this [here][1] (Biostars seems to auto edit the XML if I include it here directly) I get the following if I form ...
written 18 days ago by Mike Smith330
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Answer: A: Is biomaRt service down?
... If that website is working for you then BioMart is up working, but something isn't working in your R session. By default **biomaRt** will try to redirect you to your local mirror, which if your location is correct will be either [uswest.ensembl.org][1] or [useast.ensembl.org][2] Perhaps you can t ...
written 28 days ago by Mike Smith330
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Comment: C: R biomaRt snp_mart down?
... This was also reported on the Bioconductor support site ([https://support.bioconductor.org/p/101631/][1]), and I can confirm I'm encountering the same issues. I also run into the same problems when using the web interface, and when I try the Ensembl mirror sites, suggesting it's a problem with the ...
written 5 weeks ago by Mike Smith330
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Answer: A: Error accessing ensembl biomart via BiomaRt R package
... It looks like you're using a fairly old version of both **R** and **biomaRt** at the moment. I've made quite a few changes to the package over the past year, particularly regarding connectivity and error messages, so I'd suggest upgrading. You can keep the same version of **R** and install the lat ...
written 6 weeks ago by Mike Smith330
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Comment: C: Error accessing ensembl biomart via BiomaRt R package
... What version of **R** and **biomaRt** are you using? I suspect you might have an old version. While the [www.biomart.org][1] website still exists, it ceased to be the central reportistory for BioMart instances quite a while ago. All the defaults in the **biomaRt** package should now point to [www ...
written 6 weeks ago by Mike Smith330
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Comment: C: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
... For ease of copy/paste, the R code you would use is: geneList <- getBM(attributes = "hgnc_symbol", filters = "go_parent_term", values = go_term, mart = ensembl) ...
written 8 weeks ago by Mike Smith330
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Answer: A: Retrieving phytozome data using the R bioconductor package biomaRt
... Short answer is that I think for now you have to bypass some of the **biomaRt** functions, and create a `Mart` object yourself. So give this a try: library(biomaRt) phytozomeMart <- new("Mart", biomart = "phytozome_mart", vschema = "zome_mart" ...
written 11 weeks ago by Mike Smith330
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Comment: C: Converting between Ensembl Versions
... Version 2.33.4 of **biomaRt** now contains the function `listEnsemblArchives()` which will display all the available archives and the URL used to access them: > listEnsemblArchives() version date url [1,] "Ensembl GRCh37" "Feb 20 ...
written 3 months ago by Mike Smith330
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Answer: A: Converting between Ensembl Versions
... To answer your other question about the Ensembl archives with **biomaRt**, I think the `archive = TRUE` arguments are now long out of date. You can access mirrors using the appropriate URL to `host` and just ignoring the `archive` argument entirely e.g. for Ensembl 87 > listMarts(host = "ht ...
written 3 months ago by Mike Smith330

Latest awards to Mike Smith

Teacher 11 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
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 6 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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