User: john

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john10
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New User
Location:
United States
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3 years, 3 months ago
Joined:
3 years, 4 months ago
Email:
j*************@ucsf.edu

Posts by john

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Unimart not available in 2015?
... Thanks Thomas, this is perfect! How did you know where to find the "host" site? ...
written 3.3 years ago by john10
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Comment: C: Unimart not available in 2015?
... This is really strange. I've re-installed bioconductor and UniProt.ws package and I still get the same error. And as for your comment about overwriting the UniProt.ws function, it's not a function for me. Even after clearing R's memory and restarting: > library(UniProt.ws) Loading required pack ...
written 3.3 years ago by john10
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Comment: C: Unimart not available in 2015?
... This looks like exactly what I want. However, I'm getting an error when I run your code. I am using the most recent version of Uniprot.ws from the bioconductor packages. Do you have a more recent dev version? Here's my output: > taxId(UniProt.ws) [1] 9606 > select(UniProt.ws, "ENSG0000013961 ...
written 3.3 years ago by john10
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Comment: C: Is there a package that has Uniprot protein descriptions?
... Ah, it wasn't there when I checked earlier, and I wasn't sure if I needed to submit a new, more specific ticket. Thanks! ...
written 3.3 years ago by john10
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Is there a package that has Uniprot protein descriptions?
... With Unimart currently unavailable, is there an R package that contains protein descriptions like those available on the uniprot.org website? I've been looking through the uniprot.ws package but it doesn't look like it has the protein descriptions in it. Any help would be greatly appreciated. ...
uniprot.ws software error uniprot uniprot accessions written 3.3 years ago by john10 • updated 3.3 years ago by James W. MacDonald49k
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Comment: C: Unimart not available in 2015?
... Thanks James. I like the look of this, especially since the labels are pulled directly from the source. One thing I forgot to mention is that I would also pull the protein and gene names as well as the symbols for annotation purposes. UniProt.ws doesn't seem to have a gene name option that I'm seein ...
written 3.3 years ago by john10
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Unimart not available in 2015?
... I've used BiomaRt to map Ensemble to Entrez Id's and Uniprot Accession Id's . Recently, biomart made some changes and it seems that Unimart is no longer available? If i try this code (that was working before), i get: mart = useMart(biomart = 'unimart',dataset='uniprot',verbose = T) Space required ...
biomart uniprot unimart written 3.3 years ago by john10

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