User: Mike Smith

gravatar for Mike Smith
Mike Smith2.9k
Reputation:
2,870
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
an hour ago
Joined:
8 years, 6 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 446 results • page 2 of 45 • next >
0
votes
1
answers
64
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 6 weeks ago by Mike Smith2.9k
0
votes
2
answers
50
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 6 weeks ago by Mike Smith2.9k
0
votes
1
answers
56
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 8 weeks ago by Mike Smith2.9k
0
votes
1
answers
95
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 10 weeks ago by Mike Smith2.9k
0
votes
1
answers
56
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 11 weeks ago by Mike Smith2.9k
0
votes
3
answers
93
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 11 weeks ago by Mike Smith2.9k
0
votes
3
answers
93
views
3
answers
Answer: A: How can I get all installed Bioconductor packages?
... How about this, using the sessioninfo package: library(sessioninfo) library(dplyr) ## list all installed packages pkgs <- installed.packages()[,'Package'] ## read description files & parse using sessioninfo desc <- lapply(pkgs, utils::packageDescription) source <- vapply(desc, sessi ...
written 11 weeks ago by Mike Smith2.9k
0
votes
1
answers
175
views
1
answers
Comment: C: an error in BioMart regarding gene annotations
... The code is doing the correct thing, it's finding entries in TxDb.Hsapiens.UCSC.hg38.knownGene that overlap with your query. However, the 6 genes that keep getting returned have one coordinate incorrect in their annotation and so appear to span a huge stretch of the chromosome and overlap a lot of t ...
written 11 weeks ago by Mike Smith2.9k
0
votes
1
answers
175
views
1
answers
Comment: C: an error in BioMart regarding gene annotations
... There was presumably some something wrong in the source file used at the time of generation, as those 6 genes each span approximately 30Mb, which seems unlikely. width(gns[hits$subjectHits]) / 1e6 [1] 26.66290 36.62293 36.61152 36.61209 36.62296 36.63208 ...
written 11 weeks ago by Mike Smith2.9k
0
votes
1
answers
175
views
1
answers
Comment: C: an error in BioMart regarding gene annotations
... I don't think this is really a biomaRt question.  You're not actually querying a BioMart instance here, the annotation is found in TxDb.Hsapiens.UCSC.hg38.knownGene and the map between symbols is in org.Hs.eg.db which are both an AnnotationDb objects.  You're using biomaRt::select() but in the backg ...
written 11 weeks ago by Mike Smith2.9k

Latest awards to Mike Smith

Scholar 6 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 4 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 4 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 15 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 15 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 15 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 15 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: HDF5 reading speed
Scholar 15 months ago, created an answer that has been accepted. For A: hyperlink issue with a R package
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 15 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 15 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 15 months ago, created an answer that has been accepted. For A: Get cytoband from refsnp ID using biomaRt in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 173 users visited in the last hour