User: Mike Smith

gravatar for Mike Smith
Mike Smith2.8k
Reputation:
2,810
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
14 hours ago
Joined:
8 years, 4 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 440 results • page 1 of 44 • next >
0
votes
0
answers
25
views
0
answers
Comment: C: rhdf5 error writing matrix in hdf5 file
... Can you update your post with the output of the command sessionInfo() so we can see the versions of R and rhdf5 you're using? ...
written 1 day ago by Mike Smith2.8k
0
votes
1
answers
42
views
1
answers
Answer: A: Ensembl sheep dataset in biomaRt
... There was an issue with biomaRt that manifested when Ensembl release 91 introduced datasets with apostrophes in e.g. "Ma's Night Monkey" which would lead to the error you are seeing. See https://support.bioconductor.org/p/104025/#104043 or https://www.biostars.org/p/289654/#289861 for more details. ...
written 3 days ago by Mike Smith2.8k
0
votes
1
answers
53
views
1
answers
Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... My guess is the message Consider rerunning with 'localHub=TRUE' leads to trying this, even if it's not actually relevant. ...
written 3 days ago by Mike Smith2.8k
0
votes
0
answers
43
views
0
answers
Comment: C: CRImage createTrainingSet package is not available to install
... You can add an answer to your own question, that way other people might be able to find your solution in the future. ...
written 4 days ago by Mike Smith2.8k
0
votes
1
answers
38
views
1
answers
Answer: A: R biomaRt : listDatasets issue
... There was an issue with biomaRt that manifested when Ensembl release 91 introduced datasets with apostrophes in e.g. "Ma's Night Monkey" which would lead to the error you were seeing. See https://support.bioconductor.org/p/104025/#104043 or https://www.biostars.org/p/289654/#289861 for more details. ...
written 8 days ago by Mike Smith2.8k
0
votes
2
answers
36
views
2
answers
Answer: A: Fixing the R package error
... This is package development question and is better asked on the BioC developers mailing list  ...
written 8 days ago by Mike Smith2.8k
0
votes
1
answers
40
views
1
answers
Answer: A: cannot find function even though KEGGgraph package supposedly installed
... You need to load the library before you can use the functions it contains. Try: library(KEGGgraph) getKGMLurl("hsa00020") ...
written 22 days ago by Mike Smith2.8k
0
votes
1
answers
52
views
1
answers
Answer: A: MSGFplus: fail to load on Mac OSX 10.13.6 due to javaVersion error
... This was patched on Github in the last week https://github.com/thomasp85/MSGFplus/pull/13 I don't know if it's made its way it the version on Bioconductor yet, but you can install the Github version with: BiocInstaller::biocLite('thomasp85/MSGFplus') ...
written 4 weeks ago by Mike Smith2.8k
0
votes
1
answers
33
views
1
answers
Answer: A: biomaRt getBM() function does not recognize gene ID character vector values gene
... Your rbh column contains protein IDs, not gene IDs, so you need to change your query accordingly e.g. > getBM(attributes=c("ensembl_gene_id", "entrezgene", "hgnc_symbol", "description"), + filters="ensembl_peptide_id", + values=geneid, mart=ensembl) ensembl_gene_id entrezgene ...
written 6 weeks ago by Mike Smith2.8k
0
votes
3
answers
75
views
3
answers
Comment: C: How can I get all installed Bioconductor packages?
... I think yours has fewer steps and is easier to understand. This seems a rather neat combination: installed.packages() %>% rownames() %>% devtools:::package_info() %>% filter(source == "Bioconductor") ...
written 6 weeks ago by Mike Smith2.8k

Latest awards to Mike Smith

Scholar 10 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 3 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 3 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 13 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 13 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 13 months ago, created an answer that has been accepted. For A: hyperlink issue with a R package
Scholar 13 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 13 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 13 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 13 months ago, created an answer that has been accepted. For A: HDF5 reading speed
Scholar 13 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 13 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Scholar 13 months ago, created an answer that has been accepted. For A: Get cytoband from refsnp ID using biomaRt in R
Scholar 13 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 269 users visited in the last hour