User: Mike Smith

gravatar for Mike Smith
Mike Smith640
Reputation:
640
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
7 hours ago
Joined:
6 years, 2 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 45 results • page 1 of 5 • next >
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Answer: A: BioMart: connection fails
... As Emily has said, parts of Ensembl are down right now. This includes the archive sites and the BioMart interface at the main site. You can check this just by visiting in a browser (http://www.ensembl.org/biomart/martview?redirect=no) - at the moment you get an error page. However you can use one ...
written 3 days ago by Mike Smith640
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Answer: A: Query Genes within regions
... You're correct that a weakness of **biomaRt** is that you can't match the results with a specific part of the query, it just dumps back everything that matched at least once, and querying with each region separately isn't very quick if you have thousands of regions. If you want to do this in R, the ...
written 17 days ago by Mike Smith640
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Comment: C: Where can I download homo sapiens gene locations file including ensembl gene id,
... You can use a programmatic interface to BioMart like [biomaRt][1] and then your script records the steps you took to get the data out. [1]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 25 days ago by Mike Smith640
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Answer: A: Mapping Ensembl Gene IDs with dot suffix
... Here's an example of doing the conversion using **biomaRt**. You can use the versioned IDs you've got, but you'll see it's better the remove the version numbers. First, we'll load **biomaRt** and use your example IDs. library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsa ...
written 10 weeks ago by Mike Smith640
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Answer: A: Get gene symbols from gene ids for mouse using BioMart
... The filter you need is `mgi_symbol` e.g. library(biomaRt) ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl") mouse_gene_ids <- "0610009B22Rik" foo <- getBM(attributes=c('ensembl_gene_id', 'external_gene_name'), ...
written 11 weeks ago by Mike Smith640
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Answer: A: R ShortRead : Merge list of ShortReadQ object
... You can try using the `append()` method on the list e.g. ## List of two ShortReadQ objects with different widths > fq [[1]] class: ShortReadQ length: 256 reads; width: 36 cycles [[2]] class: ShortReadQ length: 256 reads; width: 30 cycles ## Combine to a sin ...
written 3 months ago by Mike Smith640
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Comment: C: 98.21% of input gene IDs are fail to map
... Yes look like it is. ...
written 3 months ago by Mike Smith640
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Answer: A: 98.21% of input gene IDs are fail to map
... The root of your problem is that your gene names are all upper case, but for rat (and mouse etc) generally only the first letter is capitalised, and the `bitr` conversion is case sensitive. We can use the function `str_to_title` in the **stringr** package to fix this: install.packages('stringr ...
written 3 months ago by Mike Smith640
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Answer: C: How can I uninstall my packages in Rstudio
... Remove a package with `remove.packages()` e.g. remove.packages("affycoretools") **Affycoretools** is a Bioconductor pacakge, so reinstallation needs their install script / the **BiocInstaller** package e.g. source("https://bioconductor.org/biocLite.R") biocLite("affycoretools") ...
written 3 months ago by Mike Smith640
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Comment: C: Error in BioMartVersion
... Can you update your post to include the output of `sessionInfo()` so we can see which versions of **R** and **biomaRt** you're using? I suspect your package is a little out of data, www.biomart.org hasn't been the relevant website to check for quite a while & that error message is no longer in ...
written 3 months ago by Mike Smith640

Latest awards to Mike Smith

Appreciated 14 hours ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 14 hours ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 11 weeks ago, created a post with more than 5 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
Teacher 11 weeks 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
Teacher 3 months 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 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 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
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
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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