User: Mike Smith

gravatar for Mike Smith
Mike Smith1.6k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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grimbough
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Posts by Mike Smith

<prev • 96 results • page 1 of 10 • next >
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Comment: C: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
... If you're trying to map exclusively between NCBI identifiers, it's probably best to avoid Ensembl. An Ensembl ID will always be the reference in their datasets, so you end up doing more conversions behind the scenes with more potential for non-one-to-one mappings. ...
written 5 weeks ago by Mike Smith1.6k
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Comment: C: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
... My question was really about the row ordering. Why does the 1st input value match the 3rd output, or perhaps more usefully, is there some way to also return the input values so you can at least see the pairing? ...
written 5 weeks ago by Mike Smith1.6k
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Comment: C: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
... What's the ordering of the results? For me your first input ID (`NP_001001127.1`) maps to the third line of the results (`EDNRB`) ([NCBI][1] link) [1]: https://www.ncbi.nlm.nih.gov/nuccore/NM_001001127.1?from=1&to=1320 ...
written 5 weeks ago by Mike Smith1.6k
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Comment: C: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
... I suspect if you remove the trailing `.1` from the RefSeq IDs you'll get some results from Ensembl BioMart. ...
written 5 weeks ago by Mike Smith1.6k
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Comment: C: biomaRt not finding all genes
... It would be helpful if you can give some examples of Entrez IDs that are missing in the BioMart response. ...
written 5 weeks ago by Mike Smith1.6k
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Answer: A: Accessing local installation of biomart results in "Unexpected format to the lis
... Cross posted the Bioconductor Support Site, with an answer [here][1] [1]: https://support.bioconductor.org/p/p133350/#p133424 ...
written 5 weeks ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... This code works for me at the moment,but it looks like some of the other archive sites are down (you get a 'down for maintenance' page in a browser) and will produces this same error. Hopefully this is only a temporary thing, but I think it is a server-side Ensembl issue rather than something I can ...
written 3 months ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... Currently, if I go to https://sep2019.archive.ensembl.org/ I get the message: > Server Status > The Ensembl web service you requested is temporarily unavailable. We are working to restore the service as soon as possible, and apologise for any inconvenience caused. This is a larger Ensembl is ...
written 3 months ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... This should now be fixed in biomaRt version 2.45.9. ...
written 3 months ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... This seems a weird one. If you run the function `listEnsemblArchives()` do you also get the error? That is the function that tries to read that URL, and in version 2.45.8 it should not be trying to read the `http` version. ...
written 3 months ago by Mike Smith1.6k

Latest awards to Mike Smith

Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Appreciated 3 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Teacher 3 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
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
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
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Supporter 15 months ago, voted at least 25 times.
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Appreciated 16 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 17 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 21 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 23 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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