User: Mike Smith

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Mike Smith1.2k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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19 minutes ago
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Posts by Mike Smith

<prev • 71 results • page 1 of 8 • next >
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... Try using the attribute `entrezgene_id` instead. Ensembl changed this in release 97, which only just came out (http://ftp.ensembl.org/pub/release-97/release_97_biomart_changes.txt ). ...
written 5 days ago by Mike Smith1.2k
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Answer: A: R: How to save Mart object (BiomaRt package)
... I think there's a few issues here, but the fundamental problem in your example is that `ensembl` is an object of class **Mart** not a table of results. It stores various information about the 'Mart' (which you can think of a resource) such as the URL and properties of dataset you want to access suc ...
written 16 days ago by Mike Smith1.2k
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Comment: C: vector dimension limit in biomaRt
... No need to bump this old post. You're getting lots of responses from the Ensembl team at https://www.biostars.org/p/384170/ and I responded to your cross posted query at https://support.bioconductor.org/p/121827/ ...
written 5 weeks ago by Mike Smith1.2k
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Comment: C: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
... Just want to add that you can use the `searchFilters()` function to find the appropriate filters in one step e.g. > searchFilters(m_ensembl, "exon") name description 55 ensembl_exon_id Exon ID(s) [e.g. ENSMUSE00000097910] ...
written 5 weeks ago by Mike Smith1.2k
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Answer: A: BioMart : Retrieve set_gene_id (ENSG) and set_transcript_id (ENST) from SNPs rs
... As Kevin says, you need to use the SNPs mart rather than the Genes mart. You also don't need to do this inside a loop. You can provide a vector of rsIDs to the `values` argument and the function will run the query for all of them. This will be much faster than doing them one at a time within the ...
written 6 weeks ago by Mike Smith1.2k
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Answer: A: biomaRt query Error "no upstream flank found"
... I think this is a problem with the current version of Ensembl BioMart, and I would recommending testing your code against the most recent [archive version][1]. There have been similar reports when using **biomaRt** (e.g. https://support.bioconductor.org/p/120429/), and currenty I don't think the fl ...
written 9 weeks ago by Mike Smith1.2k
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Comment: C: Finding if dbSNP type in biomart
... Nice, that's elegant. ...
written 10 weeks ago by Mike Smith1.2k
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Answer: A: Finding if dbSNP type in biomart
... You can do this using the Ensembl REST API. Here's and example in R to get the info you're looking for: library(httr) library(jsonlite) library(xml2) library(dplyr) ## the rsIDs we're interested in rs_ids <- c("rs1326880612", "rs1008829651") ## define the s ...
written 10 weeks ago by Mike Smith1.2k
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Answer: A: Biomart select rRNA sequences
... You can use the 'Gene Type' filter in Ensembl BioMart to restrict your results to a certain group. With the **biomaRt** package you'd do that via: library(biomaRt) mart <- useEnsembl('ensembl', dataset = 'rnorvegicus_gene_ensembl') biomaRt::getBM(values="rRNA", ...
written 10 weeks ago by Mike Smith1.2k
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Answer: C: Mysterious genes in my Biomart results (genes that were not part of original que
... "SPATA24" doesn't look like a normal MGI symbol since it's all in caps, so I wouldn't be suprised if your query contains "Spata24" and the all caps version is retrieved too. Is it possible your gene list include capitalised versions of the 'Trdd1' etc? I don't think BioMart is case senstive and wi ...
written 3 months ago by Mike Smith1.2k

Latest awards to Mike Smith

Teacher 16 days 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
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
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 5 months ago, created an answer with at least 3 up-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
Guru 6 months ago, received more than 100 upvotes.
Appreciated 7 months ago, created a post with more than 5 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
Good Answer 7 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
Appreciated 9 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 14 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term

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