User: Mike Smith

gravatar for Mike Smith
Mike Smith2.7k
Reputation:
2,710
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
3 hours ago
Joined:
8 years, 2 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 415 results • page 2 of 42 • next >
0
votes
0
answers
60
views
0
answers
Comment: C: Create a soft link in rhdf5
... It looks like the majority of the H5L functions are not exported by rhdf5 so I'm not sure this is possible right now. I'll see if I can address that in the near future. ...
written 26 days ago by Mike Smith2.7k
0
votes
1
answers
132
views
1
answers
Answer: A: Low level usage of rhdf5
... So this example demonstrates how to write a single column dataset containing strings of up to length 10 characters (you can set the limit). I haven't tried any of your other examples yet, but thank you for listing them. I'll create a Github issue to remind me to look at them later. I'm not sure th ...
written 26 days ago by Mike Smith2.7k
0
votes
1
answers
132
views
1
answers
Comment: C: Low level usage of rhdf5
... I see the same issue - it might take a while to get the bottom of this. It's interesting that H5T_STRING doesn't appear in the specs at https://support.hdfgroup.org/HDF5/doc1.8/RM/PredefDTypes.html You can try H5T_C_S1 but that only gives you a string of length 1 (which I guess is the null terminato ...
written 27 days ago by Mike Smith2.7k
0
votes
1
answers
70
views
1
answers
Comment: C: ensembl not working...?
... Interesting, for me this works on machine both in Europe and the US:   library(biomaRt) ensembl = useMart("ensembl", host="useast.ensembl.org", ensemblRedirect = FALSE) > dim(listDatasets(ensembl)) [1] 98 3 ...
written 27 days ago by Mike Smith2.7k
0
votes
1
answers
70
views
1
answers
Answer: A: ensembl not working...?
... It looks like you haven't posted here before, so I'll just point out that there's a couple of things you can do to increase the likelihood you get a useful answer.  The first is to make sure you tag your post with the name of the package you're trying to use - in this case that's biomaRt - so the pa ...
written 27 days ago by Mike Smith2.7k
0
votes
1
answers
71
views
1
answers
Comment: C: Cannot install Rhtslib on Mac OS 10.13
... I don't have an answer, but all those missing symbols are usually defined in zlib.  I think Rhtslib depends on zlibbioc and it should download and link automatically, but maybe try making sure it's installed already. ...
written 27 days ago by Mike Smith2.7k
0
votes
1
answers
36
views
1
answers
Answer: A: LaTeX Error with BiocWorkflowTools
... This indicates that one of the latex packages required to output the F1000 style is missing from you system, specifically mathdesign.sty. On if you're using Texlive then I think this can be found in the texlive-fonts-extra package, which on Ubuntu you can install at the command line with: apt-get ...
written 28 days ago by Mike Smith2.7k
0
votes
0
answers
39
views
0
answers
Comment: C: installing of BiomaRt package on windows 7
... Can you edit your post to include the code you used to install the package? ...
written 28 days ago by Mike Smith2.7k
0
votes
2
answers
58
views
2
answers
Answer: A: biomaRt getBM error
... If you are in the United States then it seems that the local mirror is currently down, which may be why your query is failing (you can check by visiting http://uswest.ensembl.org) You can try to force accessing the main site by using ensembl = useMart(biomart = "ensembl", host = " ...
written 29 days ago by Mike Smith2.7k
0
votes
2
answers
77
views
2
answers
Answer: A: Problems Installing biomaRt
... It looks like this problem really lies with the stringi package.  It'd suggest reinstalling that as a first try, and then re-running the biomaRt installation: install.packages('stringi') It looks like that has a system dependency on ICU4C, so if you still encounter error it may be that you need ...
written 4 weeks ago by Mike Smith2.7k

Latest awards to Mike Smith

Scholar 10 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 10 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 10 months ago, created an answer that has been accepted. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 10 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: drerio_gene_ensembl dataset missing
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"
Scholar 10 months ago, created an answer that has been accepted. For A: Get cytoband from refsnp ID using biomaRt in R
Scholar 10 months ago, created an answer that has been accepted. For A: hyperlink issue with a R package
Scholar 10 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 10 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Scholar 10 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 10 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 10 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 10 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 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: xcms and xcmsSet no longer works on my Mac
Scholar 10 months ago, created an answer that has been accepted. For A: HDF5 reading speed
Scholar 10 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 10 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Popular Question 10 months ago, created a question with more than 1,000 views. For Reading IDAT files with illuminaio
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 187 users visited in the last hour