User: Mike Smith

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Mike Smith2.5k
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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30 minutes ago
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7 years, 11 months ago
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Posts by Mike Smith

<prev • 380 results • page 1 of 38 • next >
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Comment: C: biomaRt scan error for latest assembly when indicating version Number
... It looks like http://dec2017.archive.ensembl.org redirects you to http://www.ensembl.org which I'm pretty sure was not the behaviour before the latest release - I've definitely recommended using the archive URL for the current release for exactly the reason you state. This is annoying as I recently ...
written 2 days ago by Mike Smith2.5k
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Answer: A: converting ensembl transcript ID to ensemble gene: problem & missing values
... I don't know what the 'clone_based' versions of the gene and transcript names are, but you can can get the information you want using external_gene_name and external_transcript_name respectively. You can also query using the IDs with version numbers by using ensembl_transcript_id_version as the fil ...
written 3 days ago by Mike Smith2.5k
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Answer: A: make a dash instead those gene that do not have ortologue
... Unfortunately, you can't do this directly in biomaRt, the BioMart service gives no indication of input values that don't return anything.  However you can do it yourself if you make sure you return the query values in your result - then you can see which are missing.  First off we'll set up the sam ...
written 4 days ago by Mike Smith2.5k
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Comment: C: Error retrieving data with biomaRt
... Not really sure what's going on here, but for me this works using the uniprotswissprot version e.g. library(biomaRt) mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") res <- getBM(attributes = c("mgi_symbol","uniprotswissprot"), filters = "mgi_symbol", ...
written 5 days ago by Mike Smith2.5k
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Answer: A: Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remov
... The error message and suggested installation instructions related to a system library, rather than a missing R package.  Exactly what you need to do depends upon your operating system, with suggestions given in the brackets in the message.  For example, if you're running Ubuntu 16.04 you want to ru ...
written 9 days ago by Mike Smith2.5k
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Answer: A: No BAM option in readAligned from the ShortRead package
... The readAligned function for BAM files was deprecated quite a while ago.  You should take a look at the GenomicAlignments package - there's a vignette on reading BAM files at An Introduction to the GenomicAlignments Package ...
written 9 days ago by Mike Smith2.5k
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Answer: A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
... There might be an argument you can supply to biocLite(), but one strategy is that you can list packages that are already installed with installed.packages() and you can then use that to filter your installation vector, so something like: notInstalled <- which( !listOfBiocPackages %in% rownames(in ...
written 12 days ago by Mike Smith2.5k
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Answer: A: Scan issue retrieving Drosophila Genes with biomaRt
... This is the same issue seen in https://support.bioconductor.org/p/104845/ For the host argument you need to explicitly put the 'www ', since there are many possible subdomains for ensembl.org e.g. mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "dmelanog ...
written 12 days ago by Mike Smith2.5k
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Answer: A: how to create index
... In that example ref <- system.file("extdata","reference.fa",package="Rsubread") gives the path to a file.  You can see this simply by printing it out.  For me this is > ref [1] "/g/R-devel/library/Rsubread/extdata/reference.fa" So you need to get a FASTA file for the genome you want to use, ...
written 12 days ago by Mike Smith2.5k
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Comment: C: Error in getBM--cannot connect to MySQL
... biomaRt doesn't use the mysql interface to Ensembl directly, it queries via the RESTful XML interface described here (https://www.ensembl.org/info/data/biomart/biomart_restful.html).  MySQL errors like these typically indicate some instability at the Ensembl end, rather than with the package. ...
written 16 days ago by Mike Smith2.5k

Latest awards to Mike Smith

Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: R: error while reading .h5 files from R using rdhf5 package
Appreciated 8 months ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 10 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 10 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 11 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 12 months ago, received more than 100 upvotes.
Scholar 12 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 12 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 22 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 22 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 22 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 22 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 22 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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