User: Mike Smith

gravatar for Mike Smith
Mike Smith3.3k
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3,330
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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7 hours ago
Joined:
9 years, 1 month ago
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g********@gmail.com

Posts by Mike Smith

<prev • 523 results • page 2 of 53 • next >
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Comment: C: Error in H5Fopen with kallisto .h5 files
... Does updating to **Rhdf5lib** 1.4.3 resolve this? That version was created specifically to try and fix problems with the bioconda build system. Can you also try running the command `Sys.setenv(HDF5_USE_FILE_LOCKING = "FALSE")` and then re-running whatever command is failing. If that doesn't work, ...
written 23 days ago by Mike Smith3.3k
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Comment: C: Error in H5Fopen with kallisto .h5 files
... This sounds like the issue at reported at https://github.com/pachterlab/sleuth/issues/120 and https://github.com/grimbough/Rhdf5lib/issues/15. Are you using R / Bioconductor installed via bioconda? It would be helpful if you could update your question to include the output of the command `sessionI ...
written 24 days ago by Mike Smith3.3k
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Answer: A: Add annotation, biomaRt installation
... I suspect you're missing the OpenSSL system library, and then there's a cascade of missing packages which is preventing you installing **biomaRt**. Try running the following in a terminal, and then re-running the `BiocManager::install` command. ``` sudo apt-get install libssl-dev libcurl4-openssl- ...
written 4 weeks ago by Mike Smith3.3k
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Comment: C: Pathview won't colour even with matching IDs
... Can you provide a short, self-contained, example of the code you're using? It's much easier for people to offer advice if they can start with a copy/paste example. ...
written 4 weeks ago by Mike Smith3.3k
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Answer: A: biomaRt::getBM fails with "Error in scan"
... You can't get the APPRIS status via `getSequence()` as it's on a different BioMart 'Page' to the sequence information. The web interface would prevent you from choosing these two options together, but **biomaRt** doesn't make this explicit. However, you can check the pages with the following: ``` & ...
written 5 weeks ago by Mike Smith3.3k
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Comment: C: biomaRt invalid results
... How long is the `chrpos_rsidNA` vector? It's possible you're hitting Ensembl's time limit for your query, although normally you would receive a message saying this. Does it work if you use a subset of the values in `chrpos_rsidNA`? --- As an aside, it's good to tag your question with the name of ...
written 6 weeks ago by Mike Smith3.3k
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Comment: C: Web Scraoing From Pubmd [ I want to extract gene articles form pubmed abstract
... I would take a look at the PubMed text mining API. Details are at https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/ ...
written 7 weeks ago by Mike Smith3.3k
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Comment: C: genomicFeature---paired end read::reads from the same pair were found not adjace
... Is your job really killed? That is just a warning, rather than an error, and the manual for **Rsubread** suggests that this is the expected behaviour (see Section 3 of http://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/Rsubread.pdf) ...
written 7 weeks ago by Mike Smith3.3k
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Comment: C: Error in getBM using biomaRt
... Ensembl's BioMart seems to be exceptionally slow for me at the moment - I suspect you're encountering the same problem as before, but even our smaller windows are timing out. Maybe you can try the REST API instead. The following code works similarly to before, but uses the REST API rather than Bio ...
written 8 weeks ago by Mike Smith3.3k
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Answer: A: biomart not ound some prevous release
... **biomaRt** lists the Ensembl archives found at http://www.ensembl.org/info/website/archives/index.html If the version that you want is not found there, then it has probably been permanently retired by Ensembl. You can try to contact them to see if you can obtain an offline version of the annotatio ...
written 8 weeks ago by Mike Smith3.3k

Latest awards to Mike Smith

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Scholar 4 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 5 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 5 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 8 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 11 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 22 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 22 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 22 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt is not working
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 22 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 22 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names

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